R-universe search: configuration

mlopez-ibanez

irace:Iterated Racing for Automatic Algorithm Configuration

Iterated race is an extension of the Iterated F-race method for the automatic configuration of optimization algorithms, that is, (offline) tuning their parameters by finding the most appropriate settings given a set of instances of an optimization problem. M. López-Ibáñez, J. Dubois-Lacoste, L. Pérez Cáceres, T. Stützle, and M. Birattari (2016) <doi:10.1016/j.orp.2016.09.002>.

Maintained by Manuel López-Ibáñez. Last updated 1 months ago.

algorithm-configuration hyperparameter-tuning irace optimization-algorithms

33.6 match 63 stars 10.28 score 103 scripts 1 dependents

miachol

configr:An Implementation of Parsing and Writing Configuration File (JSON/INI/YAML/TOML)

Implements the JSON, INI, YAML and TOML parser for R setting and writing of configuration file. The functionality of this package is similar to that of package 'config'.

Maintained by Jianfeng Li. Last updated 2 years ago.

configparser configuration-file ini json toml yaml

37.0 match 59 stars 8.45 score 280 scripts 5 dependents

rstudio

reticulate:Interface to 'Python'

Interface to 'Python' modules, classes, and functions. When calling into 'Python', R data types are automatically converted to their equivalent 'Python' types. When values are returned from 'Python' to R they are converted back to R types. Compatible with all versions of 'Python' >= 2.7.

Maintained by Tomasz Kalinowski. Last updated 2 days ago.

cpp

14.1 match 1.7k stars 21.07 score 18k scripts 427 dependents

r-lib

lintr:A 'Linter' for R Code

Checks adherence to a given style, syntax errors and possible semantic issues. Supports on the fly checking of R code edited with 'RStudio IDE', 'Emacs', 'Vim', 'Sublime Text', 'Atom' and 'Visual Studio Code'.

Maintained by Michael Chirico. Last updated 9 days ago.

linter

12.6 match 1.2k stars 17.00 score 916 scripts 33 dependents

r-dbi

odbc:Connect to ODBC Compatible Databases (using the DBI Interface)

A DBI-compatible interface to ODBC databases.

Maintained by Hadley Wickham. Last updated 13 days ago.

database odbc unixodbc cpp

12.8 match 396 stars 16.22 score 2.9k scripts 22 dependents

bwiernik

configural:Multivariate Profile Analysis

R functions for criterion profile analysis, Davison and Davenport (2002) <doi:10.1037/1082-989X.7.4.468> and meta-analytic criterion profile analysis, Wiernik, Wilmot, Davison, and Ones (2020) <doi:10.1037/met0000305>. Sensitivity analyses to aid in interpreting criterion profile analysis results are also included.

Maintained by Brenton M. Wiernik. Last updated 12 months ago.

51.8 match 4 stars 3.96 score 23 scripts

sparklyr

sparklyr:R Interface to Apache Spark

R interface to Apache Spark, a fast and general engine for big data processing, see <https://spark.apache.org/>. This package supports connecting to local and remote Apache Spark clusters, provides a 'dplyr' compatible back-end, and provides an interface to Spark's built-in machine learning algorithms.

Maintained by Edgar Ruiz. Last updated 10 days ago.

apache-spark distributed dplyr ide livy machine-learning remote-clusters spark sparklyr

13.5 match 959 stars 15.16 score 4.0k scripts 21 dependents

azure

azuremlsdk:Interface to the 'Azure Machine Learning' 'SDK'

Interface to the 'Azure Machine Learning' Software Development Kit ('SDK'). Data scientists can use the 'SDK' to train, deploy, automate, and manage machine learning models on the 'Azure Machine Learning' service. To learn more about 'Azure Machine Learning' visit the website: <https://docs.microsoft.com/en-us/azure/machine-learning/service/overview-what-is-azure-ml>.

Maintained by Diondra Peck. Last updated 3 years ago.

amlcompute azure azure-machine-learning azureml dsi machine-learning rstudio sdk-r

22.4 match 106 stars 8.91 score 221 scripts

rstudio

config:Manage Environment Specific Configuration Values

Manage configuration values across multiple environments (e.g. development, test, production). Read values using a function that determines the current environment and returns the appropriate value.

Maintained by Andrie de Vries. Last updated 2 months ago.

12.4 match 261 stars 15.69 score 1.8k scripts 202 dependents

r-lib

usethis:Automate Package and Project Setup

Automate package and project setup tasks that are otherwise performed manually. This includes setting up unit testing, test coverage, continuous integration, Git, 'GitHub', licenses, 'Rcpp', 'RStudio' projects, and more.

Maintained by Jennifer Bryan. Last updated 12 days ago.

github setup

9.9 match 869 stars 17.54 score 5.6k scripts 336 dependents

safetygraphics

safetyCharts:Charts for Monitoring Clinical Trial Safety

Contains chart code for monitoring clinical trial safety. Charts can be used as standalone output, but are also designed for use with the 'safetyGraphics' package, which makes it easy to load data and customize the charts using an interactive web-based interface created with Shiny.

Maintained by Jeremy Wildfire. Last updated 6 months ago.

28.4 match 9 stars 5.36 score 21 scripts 1 dependents

kwb-r

kwb.wtaq:Interface to WTAQ Drawdown Model (http://water.usgs.gov/ogw/wtaq/)

Functions enabling the writing of WTAQ input files, running of WTAQ and reading of WTAQ output files.

Maintained by Hauke Sonnenberg. Last updated 3 years ago.

drawdown-model groundwater-modelling modelling project-optiwells2 shiny-app usgs wtaq fortran

38.0 match 2 stars 3.78 score 9 scripts 1 dependents

ddimmery

tidyhte:Tidy Estimation of Heterogeneous Treatment Effects

Estimates heterogeneous treatment effects using tidy semantics on experimental or observational data. Methods are based on the doubly-robust learner of Kennedy (n.d.) <arXiv:2004.14497>. You provide a simple recipe for what machine learning algorithms to use in estimating the nuisance functions and 'tidyhte' will take care of cross-validation, estimation, model selection, diagnostics and construction of relevant quantities of interest about the variability of treatment effects.

Maintained by Drew Dimmery. Last updated 2 years ago.

25.9 match 14 stars 5.36 score 11 scripts

t-kalinowski

keras:R Interface to 'Keras'

Interface to 'Keras' <https://keras.io>, a high-level neural networks 'API'. 'Keras' was developed with a focus on enabling fast experimentation, supports both convolution based networks and recurrent networks (as well as combinations of the two), and runs seamlessly on both 'CPU' and 'GPU' devices.

Maintained by Tomasz Kalinowski. Last updated 11 months ago.

12.6 match 10.93 score 10k scripts 55 dependents

kwb-r

kwb.vs2dh:Interface to VS2DH

Interface to the open-source model USGS model VS2DH for simulation of water and energy transport in variable-saturated porous media (for more information see: http://wwwbrr.cr.usgs.gov/projects/GW_Unsat/vs2di1.3/).

Maintained by Michael Rustler. Last updated 6 years ago.

groundwater-modelling project-demeau usgs vs2dh

61.1 match 2.18 score 1 scripts 1 dependents

r-lib

httr:Tools for Working with URLs and HTTP

Useful tools for working with HTTP organised by HTTP verbs (GET(), POST(), etc). Configuration functions make it easy to control additional request components (authenticate(), add_headers() and so on).

Maintained by Hadley Wickham. Last updated 1 years ago.

api curl http

6.1 match 989 stars 20.56 score 29k scripts 4.3k dependents

ropensci

vcr:Record 'HTTP' Calls to Disk

Record test suite 'HTTP' requests and replays them during future runs. A port of the Ruby gem of the same name (<https://github.com/vcr/vcr/>). Works by hooking into the 'webmockr' R package for matching 'HTTP' requests by various rules ('HTTP' method, 'URL', query parameters, headers, body, etc.), and then caching real 'HTTP' responses on disk in 'cassettes'. Subsequent 'HTTP' requests matching any previous requests in the same 'cassette' use a cached 'HTTP' response.

Maintained by Scott Chamberlain. Last updated 13 days ago.

http https api web-services curl mock mocking http-mocking testing testing-tools tdd unit-testing vcr

12.4 match 77 stars 10.06 score 165 scripts

bioc

iSEE:Interactive SummarizedExperiment Explorer

Create an interactive Shiny-based graphical user interface for exploring data stored in SummarizedExperiment objects, including row- and column-level metadata. The interface supports transmission of selections between plots and tables, code tracking, interactive tours, interactive or programmatic initialization, preservation of app state, and extensibility to new panel types via S4 classes. Special attention is given to single-cell data in a SingleCellExperiment object with visualization of dimensionality reduction results.

Maintained by Kevin Rue-Albrecht. Last updated 11 days ago.

cellbasedassays clustering dimensionreduction featureextraction geneexpression gui immunooncology shinyapps singlecell transcription transcriptomics visualization dimension-reduction feature-extraction gene-expression hacktoberfest human-cell-atlas shiny single-cell

9.7 match 225 stars 12.86 score 380 scripts 9 dependents

r-lib

pkgconfig:Private Configuration for 'R' Packages

Set configuration options on a per-package basis. Options set by a given package only apply to that package, other packages are unaffected.

Maintained by Gábor Csárdi. Last updated 1 years ago.

9.4 match 41 stars 13.10 score 25 scripts 12k dependents

openml

OpenML:Open Machine Learning and Open Data Platform

We provide an R interface to 'OpenML.org' which is an online machine learning platform where researchers can access open data, download and upload data sets, share their machine learning tasks and experiments and organize them online to work and collaborate with other researchers. The R interface allows to query for data sets with specific properties, and allows the downloading and uploading of data sets, tasks, flows and runs. See <https://www.openml.org/guide/api> for more information.

Maintained by Giuseppe Casalicchio. Last updated 10 months ago.

arff benchmarking benchmarking-suite classification data-science database dataset datasets machine-learning machine-learning-algorithms open-data open-science opendata openml openscience regression reproducible-research statistics

10.0 match 97 stars 11.04 score 7.1k scripts

pecanproject

PEcAn.logger:Logger Functions for 'PEcAn'

Convenience functions for logging outputs from 'PEcAn', the Predictive Ecosystem Analyzer (LeBauer et al. 2017) <doi:10.1890/12-0137.1>. Enables the user to set what level of messages are printed, as well as whether these messages are written to the console, a file, or both. It also allows control over whether severe errors should stop execution of the 'PEcAn' workflow; this allows strictness when debugging and lenience when running large batches of simulations that should not be terminated by errors in individual models. It is loosely based on the 'log4j' package.

Maintained by Rob Kooper. Last updated 3 days ago.

bayesian cyberinfrastructure data-assimilation data-science ecosystem-model ecosystem-science forecasting meta-analysis national-science-foundation pecan plants

11.4 match 216 stars 9.64 score 7 scripts 40 dependents

henrikbengtsson

startup:Friendly R Startup Configuration

Adds support for R startup configuration via '.Renviron.d' and '.Rprofile.d' directories in addition to '.Renviron' and '.Rprofile' files. This makes it possible to keep private / secret environment variables separate from other environment variables. It also makes it easier to share specific startup settings by simply copying a file to a directory.

Maintained by Henrik Bengtsson. Last updated 3 months ago.

configuration environment-variables startup utility

16.6 match 166 stars 6.54 score 16 scripts

rstudio

keras3:R Interface to 'Keras'

Interface to 'Keras' <https://keras.io>, a high-level neural networks API. 'Keras' was developed with a focus on enabling fast experimentation, supports both convolution based networks and recurrent networks (as well as combinations of the two), and runs seamlessly on both CPU and GPU devices.

Maintained by Tomasz Kalinowski. Last updated 5 hours ago.

7.8 match 845 stars 13.60 score 264 scripts 2 dependents

ropensci

bowerbird:Keep a Collection of Sparkly Data Resources

Tools to get and maintain a data repository from third-party data providers.

Maintained by Ben Raymond. Last updated 5 days ago.

ropensci antarctic southern ocean data environmental satellite climate peer-reviewed

14.6 match 50 stars 7.16 score 16 scripts 1 dependents

rinterface

shinyMobile:Mobile Ready 'shiny' Apps with Standalone Capabilities

Develop outstanding 'shiny' apps for 'iOS' and 'Android' as well as beautiful 'shiny' gadgets. 'shinyMobile' is built on top of the latest 'Framework7' template <https://framework7.io>. Discover 14 new input widgets (sliders, vertical sliders, stepper, grouped action buttons, toggles, picker, smart select, ...), 2 themes (light and dark), 12 new widgets (expandable cards, badges, chips, timelines, gauges, progress bars, ...) combined with the power of server-side notifications such as alerts, modals, toasts, action sheets, sheets (and more) as well as 3 layouts (single, tabs and split).

Maintained by David Granjon. Last updated 2 months ago.

android hacktoberfest2022 pwa shiny shinyapps template

8.5 match 409 stars 11.91 score 1.1k scripts 2 dependents

datastorm-open

visNetwork:Network Visualization using 'vis.js' Library

Provides an R interface to the 'vis.js' JavaScript charting library. It allows an interactive visualization of networks.

Maintained by Benoit Thieurmel. Last updated 2 years ago.

6.6 match 549 stars 15.14 score 4.1k scripts 195 dependents

kwb-r

kwb.qmra:QMRA (quantitative microbial risk assessment)

QMRA for water supply systems.

Maintained by Michael Rustler. Last updated 4 years ago.

project-aquanes project-demoware project-smartcontrol qmra qmra-webapp-backend-engine

21.5 match 4 stars 4.53 score 21 scripts

josesamos

when:Definition of Date and Time Dimension Tables

In Multidimensional Systems the When dimension allows us to express when the analysed facts have occurred. The purpose of this package is to provide support for implementing this dimension in the form of date and time tables for Relational On-Line Analytical Processing star database systems.

Maintained by Jose Samos. Last updated 1 years ago.

openjdk

16.8 match 1 stars 5.73 score 177 scripts 2 dependents

asardaes

dtwclust:Time Series Clustering Along with Optimizations for the Dynamic Time Warping Distance

Time series clustering along with optimized techniques related to the Dynamic Time Warping distance and its corresponding lower bounds. Implementations of partitional, hierarchical, fuzzy, k-Shape and TADPole clustering are available. Functionality can be easily extended with custom distance measures and centroid definitions. Implementations of DTW barycenter averaging, a distance based on global alignment kernels, and the soft-DTW distance and centroid routines are also provided. All included distance functions have custom loops optimized for the calculation of cross-distance matrices, including parallelization support. Several cluster validity indices are included.

Maintained by Alexis Sarda. Last updated 8 months ago.

clustering dtw time-series openblas cpp

7.6 match 261 stars 12.39 score 406 scripts 14 dependents

azure

AzureVM:Virtual Machines in 'Azure'

Functionality for working with virtual machines (VMs) in Microsoft's 'Azure' cloud: <https://azure.microsoft.com/en-us/services/virtual-machines/>. Includes facilities to deploy, startup, shutdown, and cleanly delete VMs and VM clusters. Deployment configurations can be highly customised, and can make use of existing resources as well as creating new ones. A selection of predefined configurations is provided to allow easy deployment of commonly used Linux and Windows images, including Data Science Virtual Machines. With a running VM, execute scripts and install optional extensions. Part of the 'AzureR' family of packages.

Maintained by Hong Ooi. Last updated 2 years ago.

azure azure-sdk-r azure-virtual-machine data-science-virtual-machine

18.3 match 14 stars 5.05 score 16 scripts

tidyverse

googledrive:An Interface to Google Drive

Manage Google Drive files from R.

Maintained by Jennifer Bryan. Last updated 7 months ago.

google-drive

6.1 match 329 stars 14.97 score 2.1k scripts 164 dependents

ropensci

targets:Dynamic Function-Oriented 'Make'-Like Declarative Pipelines

Pipeline tools coordinate the pieces of computationally demanding analysis projects. The 'targets' package is a 'Make'-like pipeline tool for statistics and data science in R. The package skips costly runtime for tasks that are already up to date, orchestrates the necessary computation with implicit parallel computing, and abstracts files as R objects. If all the current output matches the current upstream code and data, then the whole pipeline is up to date, and the results are more trustworthy than otherwise. The methodology in this package borrows from GNU 'Make' (2015, ISBN:978-9881443519) and 'drake' (2018, <doi:10.21105/joss.00550>).

Maintained by William Michael Landau. Last updated 3 days ago.

data-science high-performance-computing make peer-reviewed pipeline r-targetopia reproducibility reproducible-research targets workflow

6.0 match 973 stars 15.20 score 4.6k scripts 22 dependents

vimc

vaultr:Vault Client for Secrets and Sensitive Data

Provides an interface to a 'HashiCorp' vault server over its http API (typically these are self-hosted; see <https://www.vaultproject.io>). This allows for secure storage and retrieval of secrets over a network, such as tokens, passwords and certificates. Authentication with vault is supported through several backends including user name/password and authentication via 'GitHub'.

Maintained by Rich FitzJohn. Last updated 1 years ago.

13.4 match 24 stars 6.78 score 2 scripts 1 dependents

tidyverse

googlesheets4:Access Google Sheets using the Sheets API V4

Interact with Google Sheets through the Sheets API v4 <https://developers.google.com/sheets/api>. "API" is an acronym for "application programming interface"; the Sheets API allows users to interact with Google Sheets programmatically, instead of via a web browser. The "v4" refers to the fact that the Sheets API is currently at version 4. This package can read and write both the metadata and the cell data in a Sheet.

Maintained by Jennifer Bryan. Last updated 8 months ago.

google-drive google-sheets spreadsheet

6.1 match 363 stars 14.55 score 7.0k scripts 144 dependents

auto-optimization

iraceplot:Plots for Visualizing the Data Produced by the 'irace' Package

Graphical visualization tools for analyzing the data produced by 'irace'. The 'iraceplot' package enables users to analyze the performance and the parameter space data sampled by the configuration during the search process. It provides a set of functions that generate different plots to visualize the configurations sampled during the execution of 'irace' and their performance. The functions just require the log file generated by 'irace' and, in some cases, they can be used with user-provided data.

Maintained by Manuel López-Ibáñez. Last updated 1 months ago.

irace parameter-tuning

15.5 match 5 stars 5.70 score 7 scripts

zarquon42b

Morpho:Calculations and Visualisations Related to Geometric Morphometrics

A toolset for Geometric Morphometrics and mesh processing. This includes (among other stuff) mesh deformations based on reference points, permutation tests, detection of outliers, processing of sliding semi-landmarks and semi-automated surface landmark placement.

Maintained by Stefan Schlager. Last updated 5 months ago.

openblas cpp openmp

8.7 match 51 stars 10.00 score 218 scripts 13 dependents

c4tb

shinyExprPortal:A Configurable 'shiny' Portal for Sharing Analysis of Molecular Expression Data

Enables deploying configuration file-based 'shiny' apps with minimal programming for interactive exploration and analysis showcase of molecular expression data. For exploration, supports visualization of correlations between rows of an expression matrix and a table of observations, such as clinical measures, and comparison of changes in expression over time. For showcase, enables visualizing the results of differential expression from package such as 'limma', co-expression modules from 'WGCNA' and lower dimensional projections.

Maintained by Rafael Henkin. Last updated 8 months ago.

bioinformatics data-analysis transcriptomics

15.6 match 5 stars 5.30 score 8 scripts

tiledb-inc

tiledb:Modern Database Engine for Complex Data Based on Multi-Dimensional Arrays

The modern database 'TileDB' introduces a powerful on-disk format for storing and accessing any complex data based on multi-dimensional arrays. It supports dense and sparse arrays, dataframes and key-values stores, cloud storage ('S3', 'GCS', 'Azure'), chunked arrays, multiple compression, encryption and checksum filters, uses a fully multi-threaded implementation, supports parallel I/O, data versioning ('time travel'), metadata and groups. It is implemented as an embeddable cross-platform C++ library with APIs from several languages, and integrations. This package provides the R support.

Maintained by Isaiah Norton. Last updated 5 days ago.

array hdfs s3 storage-manager tiledb cpp

6.9 match 107 stars 11.96 score 306 scripts 4 dependents

aggregate-genius

periscope2:Enterprise Streamlined 'shiny' Application Framework Using 'bs4Dash'

A framework for building enterprise, scalable and UI-standardized 'shiny' applications. It brings enhanced features such as 'bootstrap' v4 <https://getbootstrap.com/docs/4.0/getting-started/introduction/>, additional and enhanced 'shiny' modules, customizable UI features, as well as an enhanced application file organization paradigm. This update allows developers to harness the ability to build powerful applications and enriches the 'shiny' developers' experience when building and maintaining applications.

Maintained by Mohammed Ali. Last updated 2 months ago.

periscope shiny

12.4 match 9 stars 6.49 score 34 scripts

jakubnowicki

fixtuRes:Mock Data Generator

Generate mock data in R using YAML configuration.

Maintained by Jakub Nowicki. Last updated 3 years ago.

fixtures mock-data mock-data-generator test-data-generator yaml-configuration

16.2 match 16 stars 4.98 score 12 scripts

bioc

TPP:Analyze thermal proteome profiling (TPP) experiments

Analyze thermal proteome profiling (TPP) experiments with varying temperatures (TR) or compound concentrations (CCR).

Maintained by Dorothee Childs. Last updated 5 months ago.

immunooncology proteomics massspectrometry

16.1 match 4.98 score 16 scripts

rstudio

pointblank:Data Validation and Organization of Metadata for Local and Remote Tables

Validate data in data frames, 'tibble' objects, 'Spark' 'DataFrames', and database tables. Validation pipelines can be made using easily-readable, consecutive validation steps. Upon execution of the validation plan, several reporting options are available. User-defined thresholds for failure rates allow for the determination of appropriate reporting actions. Many other workflows are available including an information management workflow, where the aim is to record, collect, and generate useful information on data tables.

Maintained by Richard Iannone. Last updated 10 days ago.

data-assertions data-checker data-dictionaries data-frames data-inference data-management data-profiler data-quality data-validation data-verification database-tables easy-to-understand reporting-tool schema-validation testing-tools yaml-configuration

7.5 match 932 stars 10.59 score 284 scripts

ropensci

DataPackageR:Construct Reproducible Analytic Data Sets as R Packages

A framework to help construct R data packages in a reproducible manner. Potentially time consuming processing of raw data sets into analysis ready data sets is done in a reproducible manner and decoupled from the usual 'R CMD build' process so that data sets can be processed into R objects in the data package and the data package can then be shared, built, and installed by others without the need to repeat computationally costly data processing. The package maintains data provenance by turning the data processing scripts into package vignettes, as well as enforcing documentation and version checking of included data objects. Data packages can be version controlled on 'GitHub', and used to share data for manuscripts, collaboration and reproducible research.

Maintained by Dave Slager. Last updated 6 months ago.

peer-reviewed reproducibility

8.3 match 156 stars 9.38 score 72 scripts

ropensci

git2r:Provides Access to Git Repositories

Interface to the 'libgit2' library, which is a pure C implementation of the 'Git' core methods. Provides access to 'Git' repositories to extract data and running some basic 'Git' commands.

Maintained by Stefan Widgren. Last updated 12 days ago.

git git-client libgit2 libgit2-library

5.6 match 218 stars 13.86 score 836 scripts 49 dependents

bioc

artMS:Analytical R tools for Mass Spectrometry

artMS provides a set of tools for the analysis of proteomics label-free datasets. It takes as input the MaxQuant search result output (evidence.txt file) and performs quality control, relative quantification using MSstats, downstream analysis and integration. artMS also provides a set of functions to re-format and make it compatible with other analytical tools, including, SAINTq, SAINTexpress, Phosfate, and PHOTON. Check [http://artms.org](http://artms.org) for details.

Maintained by David Jimenez-Morales. Last updated 5 months ago.

proteomics differentialexpression biomedicalinformatics systemsbiology massspectrometry annotation qualitycontrol genesetenrichment clustering normalization immunooncology multiplecomparison analysis analytical ap-ms bioconductor bioinformatics mass-spectrometry phosphoproteomics post-translational-modification quantitative-analysis

12.1 match 14 stars 6.41 score 13 scripts

mlr-org

mlr3tuning:Hyperparameter Optimization for 'mlr3'

Hyperparameter optimization package of the 'mlr3' ecosystem. It features highly configurable search spaces via the 'paradox' package and finds optimal hyperparameter configurations for any 'mlr3' learner. 'mlr3tuning' works with several optimization algorithms e.g. Random Search, Iterated Racing, Bayesian Optimization (in 'mlr3mbo') and Hyperband (in 'mlr3hyperband'). Moreover, it can automatically optimize learners and estimate the performance of optimized models with nested resampling.

Maintained by Marc Becker. Last updated 3 months ago.

bbotk hyperparameter-optimization hyperparameter-tuning machine-learning mlr3 optimization tune tuning

6.6 match 55 stars 11.59 score 384 scripts 11 dependents

nano-optics

planar:Multilayer Optics

Solves the electromagnetic problem of reflection and transmission at a planar multilayer interface. Also computed are the decay rates and emission profile for a dipolar emitter.

Maintained by Baptiste Auguié. Last updated 3 years ago.

openblas cpp

13.0 match 7 stars 5.83 score 65 scripts

plotly

plotly:Create Interactive Web Graphics via 'plotly.js'

Create interactive web graphics from 'ggplot2' graphs and/or a custom interface to the (MIT-licensed) JavaScript library 'plotly.js' inspired by the grammar of graphics.

Maintained by Carson Sievert. Last updated 3 months ago.

d3js data-visualization ggplot2 javascript plotly shiny webgl

3.9 match 2.6k stars 19.43 score 93k scripts 797 dependents

umr-amap

AMAPVox:LiDAR Data Voxelisation

Read, manipulate and write voxel spaces. Voxel spaces are read from text-based output files of the 'AMAPVox' software. 'AMAPVox' is a LiDAR point cloud voxelisation software that aims at estimating leaf area through several theoretical/numerical approaches. See more in the article Vincent et al. (2017) <doi:10.23708/1AJNMP> and the technical note Vincent et al. (2021) <doi:10.23708/1AJNMP>.

Maintained by Philippe Verley. Last updated 2 months ago.

11.7 match 15 stars 6.35 score 12 scripts

dallenmidd

IxPopDyMod:Framework for Tick Population and Infection Modeling

Code to specify, run, and then visualize and analyze the results of Ixodidae (hard-bodied ticks) population and infection dynamics models. Such models exist in the literature, but the source code to run them is not always available. 'IxPopDyMod' provides an easy way for these models to be written and shared.

Maintained by Myles Stokowski. Last updated 4 months ago.

24.7 match 2 stars 3.00 score 6 scripts

markedmondson1234

googleAuthR:Authenticate and Create Google APIs

Create R functions that interact with OAuth2 Google APIs <https://developers.google.com/apis-explorer/> easily, with auto-refresh and Shiny compatibility.

Maintained by Erik Grönroos. Last updated 10 months ago.

api authentication google googleauthr oauth2-flow shiny

5.8 match 178 stars 12.84 score 804 scripts 13 dependents

r-lib

gmailr:Access the 'Gmail' 'RESTful' API

An interface to the 'Gmail' 'RESTful' API. Allows access to your 'Gmail' messages, threads, drafts and labels.

Maintained by Jennifer Bryan. Last updated 1 years ago.

6.3 match 230 stars 11.49 score 289 scripts 1 dependents

rstudio

tfestimators:Interface to 'TensorFlow' Estimators

Interface to 'TensorFlow' Estimators <https://www.tensorflow.org/guide/estimator>, a high-level API that provides implementations of many different model types including linear models and deep neural networks.

Maintained by Tomasz Kalinowski. Last updated 3 years ago.

8.5 match 57 stars 8.42 score 170 scripts

bmoretz

dyn.log:Dynamic Logging for R Inspired by Configuration Driven Development

A comprehensive and dynamic configuration driven logging package for R. While there are several excellent logging solutions already in the R ecosystem, I always feel constrained in some way by each of them. Every project is designed differently to solve it's domain specific problem, and ultimately the utility of a logging solution is its ability to adapt to this design. This is the raison d'être for 'dyn.log': to provide a modular design, template mechanics and a configuration-based integration model, so that the logger can integrate deeply into your design, even though it knows nothing about it.

Maintained by Brandon Moretz. Last updated 3 years ago.

logging

14.9 match 1 stars 4.78 score 10 scripts

mrc-ide

rrq:Simple Redis Queue

Simple Redis queue in R.

Maintained by Rich FitzJohn. Last updated 4 months ago.

cluster infrastructure

9.3 match 24 stars 7.40 score 14 scripts 3 dependents

jkcshea

ivmte:Instrumental Variables: Extrapolation by Marginal Treatment Effects

The marginal treatment effect was introduced by Heckman and Vytlacil (2005) <doi:10.1111/j.1468-0262.2005.00594.x> to provide a choice-theoretic interpretation to instrumental variables models that maintain the monotonicity condition of Imbens and Angrist (1994) <doi:10.2307/2951620>. This interpretation can be used to extrapolate from the compliers to estimate treatment effects for other subpopulations. This package provides a flexible set of methods for conducting this extrapolation. It allows for parametric or nonparametric sieve estimation, and allows the user to maintain shape restrictions such as monotonicity. The package operates in the general framework developed by Mogstad, Santos and Torgovitsky (2018) <doi:10.3982/ECTA15463>, and accommodates either point identification or partial identification (bounds). In the partially identified case, bounds are computed using either linear programming or quadratically constrained quadratic programming. Support for four solvers is provided. Gurobi and the Gurobi R API can be obtained from <http://www.gurobi.com/index>. CPLEX can be obtained from <https://www.ibm.com/analytics/cplex-optimizer>. CPLEX R APIs 'Rcplex' and 'cplexAPI' are available from CRAN. MOSEK and the MOSEK R API can be obtained from <https://www.mosek.com/>. The lp_solve library is freely available from <http://lpsolve.sourceforge.net/5.5/>, and is included when installing its API 'lpSolveAPI', which is available from CRAN.

Maintained by Joshua Shea. Last updated 7 months ago.

12.7 match 18 stars 5.33 score 30 scripts

usdaforestservice

gdalraster:Bindings to the 'Geospatial Data Abstraction Library' Raster API

Interface to the Raster API of the 'Geospatial Data Abstraction Library' ('GDAL', <https://gdal.org>). Bindings are implemented in an exposed C++ class encapsulating a 'GDALDataset' and its raster band objects, along with several stand-alone functions. These support manual creation of uninitialized datasets, creation from existing raster as template, read/set dataset parameters, low level I/O, color tables, raster attribute tables, virtual raster (VRT), and 'gdalwarp' wrapper for reprojection and mosaicing. Includes 'GDAL' algorithms ('dem_proc()', 'polygonize()', 'rasterize()', etc.), and functions for coordinate transformation and spatial reference systems. Calling signatures resemble the native C, C++ and Python APIs provided by the 'GDAL' project. Includes raster 'calc()' to evaluate a given R expression on a layer or stack of layers, with pixel x/y available as variables in the expression; and raster 'combine()' to identify and count unique pixel combinations across multiple input layers, with optional output of the pixel-level combination IDs. Provides raster display using base 'graphics'. Bindings to a subset of the 'OGR' API are also included for managing vector data sources. Bindings to a subset of the Virtual Systems Interface ('VSI') are also included to support operations on 'GDAL' virtual file systems. These are general utility functions that abstract file system operations on URLs, cloud storage services, 'Zip'/'GZip'/'7z'/'RAR' archives, and in-memory files. 'gdalraster' may be useful in applications that need scalable, low-level I/O, or prefer a direct 'GDAL' API.

Maintained by Chris Toney. Last updated 13 hours ago.

gdal geospatial raster vector cpp

7.1 match 42 stars 9.52 score 32 scripts 3 dependents

tudo-r

BatchJobs:Batch Computing with R

Provides Map, Reduce and Filter variants to generate jobs on batch computing systems like PBS/Torque, LSF, SLURM and Sun Grid Engine. Multicore and SSH systems are also supported. For further details see the project web page.

Maintained by Bernd Bischl. Last updated 3 years ago.

7.8 match 85 stars 8.57 score 616 scripts 3 dependents

nimble-dev

nimble:MCMC, Particle Filtering, and Programmable Hierarchical Modeling

A system for writing hierarchical statistical models largely compatible with 'BUGS' and 'JAGS', writing nimbleFunctions to operate models and do basic R-style math, and compiling both models and nimbleFunctions via custom-generated C++. 'NIMBLE' includes default methods for MCMC, Laplace Approximation, Monte Carlo Expectation Maximization, and some other tools. The nimbleFunction system makes it easy to do things like implement new MCMC samplers from R, customize the assignment of samplers to different parts of a model from R, and compile the new samplers automatically via C++ alongside the samplers 'NIMBLE' provides. 'NIMBLE' extends the 'BUGS'/'JAGS' language by making it extensible: New distributions and functions can be added, including as calls to external compiled code. Although most people think of MCMC as the main goal of the 'BUGS'/'JAGS' language for writing models, one can use 'NIMBLE' for writing arbitrary other kinds of model-generic algorithms as well. A full User Manual is available at <https://r-nimble.org>.

Maintained by Christopher Paciorek. Last updated 5 days ago.

bayesian-inference bayesian-methods hierarchical-models mcmc probabilistic-programming openblas cpp

5.0 match 169 stars 12.97 score 2.6k scripts 19 dependents

coolbutuseless

yyjsonr:Fast 'JSON', 'NDJSON' and 'GeoJSON' Parser and Generator

A fast 'JSON' parser, generator and validator which converts 'JSON', 'NDJSON' (Newline Delimited 'JSON') and 'GeoJSON' (Geographic 'JSON') data to/from R objects. The standard R data types are supported (e.g. logical, numeric, integer) with configurable handling of NULL and NA values. Data frames, atomic vectors and lists are all supported as data containers translated to/from 'JSON'. 'GeoJSON' data is read in as 'simple features' objects. This implementation wraps the 'yyjson' 'C' library which is available from <https://github.com/ibireme/yyjson>.

Maintained by Mike Cheng. Last updated 4 months ago.

zlib

6.8 match 147 stars 9.56 score 22 scripts 9 dependents

wadpac

GGIR:Raw Accelerometer Data Analysis

A tool to process and analyse data collected with wearable raw acceleration sensors as described in Migueles and colleagues (JMPB 2019), and van Hees and colleagues (JApplPhysiol 2014; PLoSONE 2015). The package has been developed and tested for binary data from 'GENEActiv' <https://activinsights.com/>, binary (.gt3x) and .csv-export data from 'Actigraph' <https://theactigraph.com> devices, and binary (.cwa) and .csv-export data from 'Axivity' <https://axivity.com>. These devices are currently widely used in research on human daily physical activity. Further, the package can handle accelerometer data file from any other sensor brand providing that the data is stored in csv format. Also the package allows for external function embedding.

Maintained by Vincent T van Hees. Last updated 3 days ago.

accelerometer activity-recognition circadian-rhythm movement-sensor sleep

4.8 match 109 stars 13.20 score 342 scripts 3 dependents

shikokuchuo

mirai:Minimalist Async Evaluation Framework for R

Designed for simplicity, a 'mirai' evaluates an R expression asynchronously in a parallel process, locally or distributed over the network. The result is automatically available upon completion. Modern networking and concurrency, built on 'nanonext' and 'NNG' (Nanomsg Next Gen), ensures reliable and efficient scheduling over fast inter-process communications or TCP/IP secured by TLS. Distributed computing can launch remote resources via SSH or cluster managers. An inherently queued architecture handles many more tasks than available processes, and requires no storage on the file system. Innovative features include support for otherwise non-exportable reference objects, event-driven promises, and asynchronous parallel map.

Maintained by Charlie Gao. Last updated 3 days ago.

async asynchronous-tasks concurrency distributed-computing high-performance-computing parallel-computing

5.3 match 217 stars 11.94 score 130 scripts 7 dependents

montesmariana

glossr:Use Interlinear Glosses in R Markdown

Read examples with interlinear glosses from files or from text and print them in a way compatible with both Latex and HTML outputs.

Maintained by Mariana Montes. Last updated 10 months ago.

9.5 match 13 stars 6.31 score 26 scripts

bdhitt

binGroup2:Identification and Estimation using Group Testing

Methods for the group testing identification problem: 1) Operating characteristics (e.g., expected number of tests) for commonly used hierarchical and array-based algorithms, and 2) Optimal testing configurations for these same algorithms. Methods for the group testing estimation problem: 1) Estimation and inference procedures for an overall prevalence, and 2) Regression modeling for commonly used hierarchical and array-based algorithms.

Maintained by Brianna Hitt. Last updated 1 years ago.

openblas cpp

24.2 match 2.48 score 3 scripts 1 dependents

cran

snowfall:Easier Cluster Computing (Based on 'snow')

Usability wrapper around snow for easier development of parallel R programs. This package offers e.g. extended error checks, and additional functions. All functions work in sequential mode, too, if no cluster is present or wished. Package is also designed as connector to the cluster management tool sfCluster, but can also used without it.

Maintained by Jochen Knaus. Last updated 1 years ago.

7.5 match 7.89 score 1.8k scripts 48 dependents

project-gen3sis

gen3sis:General Engine for Eco-Evolutionary Simulations

Contains an engine for spatially-explicit eco-evolutionary mechanistic models with a modular implementation and several support functions. It allows exploring the consequences of ecological and macroevolutionary processes across realistic or theoretical spatio-temporal landscapes on biodiversity patterns as a general term. Reference: Oskar Hagen, Benjamin Flueck, Fabian Fopp, Juliano S. Cabral, Florian Hartig, Mikael Pontarp, Thiago F. Rangel, Loic Pellissier (2021) "gen3sis: A general engine for eco-evolutionary simulations of the processes that shape Earth's biodiversity" <doi:10.1371/journal.pbio.3001340>.

Maintained by Oskar Hagen. Last updated 1 years ago.

biodiversity ecology evolution mechanistic model modeling simulation cpp

7.8 match 29 stars 7.56 score 69 scripts

mrc-ide

orderly2:Orderly Next Generation

Distributed reproducible computing framework, adopting ideas from git, docker and other software. By defining a lightweight interface around the inputs and outputs of an analysis, a lot of the repetitive work for reproducible research can be automated. We define a simple format for organising and describing work that facilitates collaborative reproducible research and acknowledges that all analyses are run multiple times over their lifespans.

Maintained by Rich FitzJohn. Last updated 2 months ago.

7.0 match 8 stars 8.30 score 49 scripts 2 dependents

mathiasambuehl

cna:Causal Modeling with Coincidence Analysis

Provides comprehensive functionalities for causal modeling with Coincidence Analysis (CNA), which is a configurational comparative method of causal data analysis that was first introduced in Baumgartner (2009) <doi:10.1177/0049124109339369>, and generalized in Baumgartner & Ambuehl (2018) <doi:10.1017/psrm.2018.45>. CNA is designed to recover INUS-causation from data, which is particularly relevant for analyzing processes featuring conjunctural causation (component causation) and equifinality (alternative causation). CNA is currently the only method for INUS-discovery that allows for multiple effects (outcomes/endogenous factors), meaning it can analyze common-cause and causal chain structures.

Maintained by Mathias Ambuehl. Last updated 8 months ago.

cpp

12.1 match 1 stars 4.78 score 45 scripts 3 dependents

thewileylab

ReviewR:A Light-Weight, Portable Tool for Reviewing Individual Patient Records

A portable Shiny tool to explore patient-level electronic health record data and perform chart review in a single integrated framework. This tool supports browsing clinical data in many different formats including multiple versions of the 'OMOP' common data model as well as the 'MIMIC-III' data model. In addition, chart review information is captured and stored securely via the Shiny interface in a 'REDCap' (Research Electronic Data Capture) project using the 'REDCap' API. See the 'ReviewR' website for additional information, documentation, and examples.

Maintained by David Mayer. Last updated 2 years ago.

9.1 match 24 stars 6.33 score 6 scripts

momx

Momocs:Morphometrics using R

The goal of 'Momocs' is to provide a complete, convenient, reproducible and open-source toolkit for 2D morphometrics. It includes most common 2D morphometrics approaches on outlines, open outlines, configurations of landmarks, traditional morphometrics, and facilities for data preparation, manipulation and visualization with a consistent grammar throughout. It allows reproducible, complex morphometrics analyses and other morphometrics approaches should be easy to plug in, or develop from, on top of this canvas.

Maintained by Vincent Bonhomme. Last updated 1 years ago.

morphometrics

7.7 match 51 stars 7.42 score 346 scripts

vimc

orderly:Lightweight Reproducible Reporting

Order, create and store reports from R. By defining a lightweight interface around the inputs and outputs of an analysis, a lot of the repetitive work for reproducible research can be automated. We define a simple format for organising and describing work that facilitates collaborative reproducible research and acknowledges that all analyses are run multiple times over their lifespans.

Maintained by Rich FitzJohn. Last updated 2 years ago.

5.9 match 117 stars 9.63 score 94 scripts 4 dependents

ropensci

gert:Simple Git Client for R

Simple git client for R based on 'libgit2' <https://libgit2.org> with support for SSH and HTTPS remotes. All functions in 'gert' use basic R data types (such as vectors and data-frames) for their arguments and return values. User credentials are shared with command line 'git' through the git-credential store and ssh keys stored on disk or ssh-agent.

Maintained by Jeroen Ooms. Last updated 5 months ago.

libgit2

3.8 match 154 stars 14.82 score 158 scripts 369 dependents

meo265

loggit2:Easy-to-Use, Dependencyless Logger

An easy-to-use 'ndjson' (newline-delimited 'JSON') logger. It provides a set of wrappers for base R's message(), warning(), and stop() functions that maintain identical functionality, but also log the handler message to an 'ndjson' log file. No change in existing code is necessary to use this package, and only a few additional adjustments are needed to fully utilize its potential.

Maintained by Matthias Ollech. Last updated 9 days ago.

logger logging cpp

9.5 match 2 stars 5.75 score 1 scripts

johnaponte

repana:Repeatable Analysis in R

Set of utilities to facilitate the reproduction of analysis in R. It allow to make_structure(), clean_structure(), and run and log programs in a predefined order to allow secondary files, analysis and reports be constructed in an ordered and reproducible form.

Maintained by John J. Aponte. Last updated 23 days ago.

9.1 match 5 stars 5.98 score 19 scripts

r-spatial

qgisprocess:Use 'QGIS' Processing Algorithms

Provides seamless access to the 'QGIS' (<https://qgis.org>) processing toolbox using the standalone 'qgis_process' command-line utility. Both native and third-party (plugin) processing providers are supported. Beside referring data sources from file, also common objects from 'sf', 'terra' and 'stars' are supported. The native processing algorithms are documented by QGIS.org (2024) <https://docs.qgis.org/latest/en/docs/user_manual/processing_algs/>.

Maintained by Floris Vanderhaeghe. Last updated 5 months ago.

5.4 match 210 stars 10.09 score 175 scripts

bioc

pipeFrame:Pipeline framework for bioinformatics in R

pipeFrame is an R package for building a componentized bioinformatics pipeline. Each step in this pipeline is wrapped in the framework, so the connection among steps is created seamlessly and automatically. Users could focus more on fine-tuning arguments rather than spending a lot of time on transforming file format, passing task outputs to task inputs or installing the dependencies. Componentized step elements can be customized into other new pipelines flexibly as well. This pipeline can be split into several important functional steps, so it is much easier for users to understand the complex arguments from each step rather than parameter combination from the whole pipeline. At the same time, componentized pipeline can restart at the breakpoint and avoid rerunning the whole pipeline, which may save a lot of time for users on pipeline tuning or such issues as power off or process other interrupts.

Maintained by Zheng Wei. Last updated 5 months ago.

software infrastructure workflowstep

13.3 match 1 stars 4.08 score 2 scripts 1 dependents

safetygraphics

safetyGraphics:Interactive Graphics for Monitoring Clinical Trial Safety

A framework for evaluation of clinical trial safety. Users can interactively explore their data using the included 'Shiny' application.

Maintained by Jeremy Wildfire. Last updated 2 years ago.

6.6 match 98 stars 8.18 score 111 scripts

vincentarelbundock

tinytable:Simple and Configurable Tables in 'HTML', 'LaTeX', 'Markdown', 'Word', 'PNG', 'PDF', and 'Typst' Formats

Create highly customized tables with this simple and dependency-free package. Data frames can be converted to 'HTML', 'LaTeX', 'Markdown', 'Word', 'PNG', 'PDF', or 'Typst' tables. The user interface is minimalist and easy to learn. The syntax is concise. 'HTML' tables can be customized using the flexible 'Bootstrap' framework, and 'LaTeX' code with the 'tabularray' package.

Maintained by Vincent Arel-Bundock. Last updated 10 hours ago.

4.4 match 263 stars 12.23 score 562 scripts 10 dependents

bioc

AnVIL:Bioconductor on the AnVIL compute environment

The AnVIL is a cloud computing resource developed in part by the National Human Genome Research Institute. The AnVIL package provides end-user and developer functionality. For the end-user, AnVIL provides fast binary package installation, utitlities for working with Terra / AnVIL table and data resources, and convenient functions for file movement to and from Google cloud storage. For developers, AnVIL provides programatic access to the Terra, Leonardo, Rawls, and Dockstore RESTful programming interface, including helper functions to transform JSON responses to formats more amenable to manipulation in R.

Maintained by Marcel Ramos. Last updated 24 days ago.

infrastructure

6.0 match 8.80 score 250 scripts 10 dependents

joachim-gassen

ExPanDaR:Explore Your Data Interactively

Provides a shiny-based front end (the 'ExPanD' app) and a set of functions for exploratory data analysis. Run as a web-based app, 'ExPanD' enables users to assess the robustness of empirical evidence without providing them access to the underlying data. You can export a notebook containing the analysis of 'ExPanD' and/or use the functions of the package to support your exploratory data analysis workflow. Refer to the vignettes of the package for more information on how to use 'ExPanD' and/or the functions of this package.

Maintained by Joachim Gassen. Last updated 4 years ago.

accounting eda exploratory-data-analysis finance open-science replication shiny shiny-apps

6.8 match 156 stars 7.80 score 203 scripts

r-world-devs

cohortBuilder:Data Source Agnostic Filtering Tools

Common API for filtering data stored in different data models. Provides multiple filter types and reproducible R code. Works standalone or with 'shinyCohortBuilder' as the GUI for interactive Shiny apps.

Maintained by Krystian Igras. Last updated 5 days ago.

6.5 match 8 stars 7.98 score 55 scripts 1 dependents

flippiecoetser

Environment:Manage Environment Variables

Get or Set Environment Variables using .Renviron configuration file.

Maintained by Flippie Coetser. Last updated 9 days ago.

configuration environment

15.6 match 1 stars 3.35 score 74 scripts 1 dependents

iandryden

shapes:Statistical Shape Analysis

Routines for the statistical analysis of landmark shapes, including Procrustes analysis, graphical displays, principal components analysis, permutation and bootstrap tests, thin-plate spline transformation grids and comparing covariance matrices. See Dryden, I.L. and Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd Edition), John Wiley and Sons.

Maintained by Ian Dryden. Last updated 4 months ago.

6.1 match 7 stars 8.50 score 225 scripts 24 dependents

mlr-org

mlr3torch:Deep Learning with 'mlr3'

Deep Learning library that extends the mlr3 framework by building upon the 'torch' package. It allows to conveniently build, train, and evaluate deep learning models without having to worry about low level details. Custom architectures can be created using the graph language defined in 'mlr3pipelines'.

Maintained by Sebastian Fischer. Last updated 1 months ago.

data-science deep-learning machine-learning mlr3 torch

6.8 match 42 stars 7.63 score 78 scripts

mrc-ide

hipercow:High Performance Computing

Set up cluster environments and jobs. Moo.

Maintained by Rich FitzJohn. Last updated 12 days ago.

7.9 match 1 stars 6.53 score 45 scripts 1 dependents

ralmond

Proc4:Four Process Assessment Database and Dispatcher

Utilities for working with messages in the four four process architecture as json objects.

Maintained by Russell Almond. Last updated 1 years ago.

assessment-scoring evidence-centered-design mongodb-database

12.8 match 3.95 score 2 dependents

act-org

RSCAT:Shadow-Test Approach to Computerized Adaptive Testing

As an advanced approach to computerized adaptive testing (CAT), shadow testing (van der Linden(2005) <doi:10.1007/0-387-29054-0>) dynamically assembles entire shadow tests as a part of selecting items throughout the testing process. Selecting items from shadow tests guarantees the compliance of all content constraints defined by the blueprint. 'RSCAT' is an R package for the shadow-test approach to CAT. The objective of 'RSCAT' is twofold: 1) Enhancing the effectiveness of shadow-test CAT simulation; 2) Contributing to the academic and scientific community for CAT research. RSCAT is currently designed for dichotomous items based on the three-parameter logistic (3PL) model.

Maintained by Bingnan Jiang. Last updated 3 years ago.

computerized-adaptive-testing item-response-theory java mixed-integer-programming open-source optimization shadow-testing shiny xpress-mosel openjdk

14.0 match 7 stars 3.54 score 6 scripts

ropensci

virtuoso:Interface to 'Virtuoso' using 'ODBC'

Provides users with a simple and convenient mechanism to manage and query a 'Virtuoso' database using the 'DBI' (Data-Base Interface) compatible 'ODBC' (Open Database Connectivity) interface. 'Virtuoso' is a high-performance "universal server," which can act as both a relational database, supporting standard Structured Query Language ('SQL') queries, while also supporting data following the Resource Description Framework ('RDF') model for Linked Data. 'RDF' data can be queried using 'SPARQL' ('SPARQL' Protocol and 'RDF' Query Language) queries, a graph-based query that supports semantic reasoning. This allows users to leverage the performance of local or remote 'Virtuoso' servers using popular 'R' packages such as 'DBI' and 'dplyr', while also providing a high-performance solution for working with large 'RDF' 'triplestores' from 'R.' The package also provides helper routines to install, launch, and manage a 'Virtuoso' server locally on 'Mac', 'Windows' and 'Linux' platforms using the standard interactive installers from the 'R' command-line. By automatically handling these setup steps, the package can make using 'Virtuoso' considerably faster and easier for a most users to deploy in a local environment. Managing the bulk import of triples from common serializations with a single intuitive command is another key feature of this package. Bulk import performance can be tens to hundreds of times faster than the comparable imports using existing 'R' tools, including 'rdflib' and 'redland' packages.

Maintained by Carl Boettiger. Last updated 11 months ago.

8.8 match 9 stars 5.61 score 15 scripts

manuelhentschel

vscDebugger:Support for Visual Studio Code Debugger

Provides support for a visual studio code debugger

Maintained by Manuel Hentschel. Last updated 2 days ago.

debugger vscode

7.0 match 95 stars 7.00 score 15 scripts

davidgohel

gdtools:Utilities for Graphical Rendering and Fonts Management

Tools are provided to compute metrics of formatted strings and to check the availability of a font. Another set of functions is provided to support the collection of fonts from 'Google Fonts' in a cache. Their use is simple within 'R Markdown' documents and 'shiny' applications but also with graphic productions generated with the 'ggiraph', 'ragg' and 'svglite' packages or with tabular productions from the 'flextable' package.

Maintained by David Gohel. Last updated 2 months ago.

cairo freetype cpp

3.8 match 27 stars 12.80 score 234 scripts 144 dependents

r-dbi

bigrquery:An Interface to Google's 'BigQuery' 'API'

Easily talk to Google's 'BigQuery' database from R.

Maintained by Hadley Wickham. Last updated 20 days ago.

bigquery database cpp

3.9 match 520 stars 12.55 score 1.8k scripts 4 dependents

calvagone

campsis:Generic PK/PD Simulation Platform CAMPSIS

A generic, easy-to-use and intuitive pharmacokinetic/pharmacodynamic (PK/PD) simulation platform based on R packages 'rxode2' and 'mrgsolve'. CAMPSIS provides an abstraction layer over the underlying processes of writing a PK/PD model, assembling a custom dataset and running a simulation. CAMPSIS has a strong dependency to the R package 'campsismod', which allows to read/write a model from/to files and adapt it further on the fly in the R environment. Package 'campsis' allows the user to assemble a dataset in an intuitive manner. Once the user’s dataset is ready, the package is in charge of preparing the simulation, calling 'rxode2' or 'mrgsolve' (at the user's choice) and returning the results, for the given model, dataset and desired simulation settings.

Maintained by Nicolas Luyckx. Last updated 1 months ago.

6.5 match 8 stars 7.52 score 93 scripts

ropensci

rix:Reproducible Data Science Environments with 'Nix'

Simplifies the creation of reproducible data science environments using the 'Nix' package manager, as described in Dolstra (2006) <ISBN 90-393-4130-3>. The included `rix()` function generates a complete description of the environment as a `default.nix` file, which can then be built using 'Nix'. This results in project specific software environments with pinned versions of R, packages, linked system dependencies, and other tools. Additional helpers make it easy to run R code in 'Nix' software environments for testing and production.

Maintained by Bruno Rodrigues. Last updated 5 days ago.

nix peer-reviewed reproducibility reproducible-research

4.6 match 235 stars 10.54 score 67 scripts

atlasoflivingaustralia

galah:Biodiversity Data from the GBIF Node Network

The Global Biodiversity Information Facility ('GBIF', <https://www.gbif.org>) sources data from an international network of data providers, known as 'nodes'. Several of these nodes - the "living atlases" (<https://living-atlases.gbif.org>) - maintain their own web services using software originally developed by the Atlas of Living Australia ('ALA', <https://www.ala.org.au>). 'galah' enables the R community to directly access data and resources hosted by 'GBIF' and its partner nodes.

Maintained by Martin Westgate. Last updated 1 months ago.

5.2 match 43 stars 9.17 score 275 scripts 1 dependents

jeroen

curl:A Modern and Flexible Web Client for R

Bindings to 'libcurl' <https://curl.se/libcurl/> for performing fully configurable HTTP/FTP requests where responses can be processed in memory, on disk, or streaming via the callback or connection interfaces. Some knowledge of 'libcurl' is recommended; for a more-user-friendly web client see the 'httr2' package which builds on this package with http specific tools and logic.

Maintained by Jeroen Ooms. Last updated 23 days ago.

curl

2.4 match 224 stars 19.98 score 4.0k scripts 5.9k dependents

ggpmxdevelopment

ggPMX:'ggplot2' Based Tool to Facilitate Diagnostic Plots for NLME Models

At Novartis, we aimed at standardizing the set of diagnostic plots used for modeling activities in order to reduce the overall effort required for generating such plots. For this, we developed a guidance that proposes an adequate set of diagnostics and a toolbox, called 'ggPMX' to execute them. 'ggPMX' is a toolbox that can generate all diagnostic plots at a quality sufficient for publication and submissions using few lines of code. This package focuses on plots recommended by ISoP <doi:10.1002/psp4.12161>. While not required, you can get/install the 'R' 'lixoftConnectors' package in the 'Monolix' installation, as described at the following url <https://monolix.lixoft.com/monolix-api/lixoftconnectors_installation/>. When 'lixoftConnectors' is available, 'R' can use 'Monolix' directly to create the required Chart Data instead of exporting it from the 'Monolix' gui.

Maintained by Matthew Fidler. Last updated 1 years ago.

pharmacometrics pmx reporting

6.5 match 39 stars 7.23 score 80 scripts

gmod

JBrowseR:An R Interface to the JBrowse 2 Genome Browser

Provides an R interface to the JBrowse 2 genome browser. Enables embedding a JB2 genome browser in a Shiny app or R Markdown document. The browser can also be launched from an interactive R console. The browser can be loaded with a variety of common genomics data types, and can be used with a custom theme.

Maintained by Colin Diesh. Last updated 1 years ago.

genomics reactjs rmarkdown shiny visualization

6.8 match 35 stars 6.81 score 31 scripts 1 dependents

alexander-pastukhov

BiDimRegression:Calculates the Bidimensional Regression Between Two 2D Configurations

Calculates the bidimensional regression between two 2D configurations following the approach by Tobler (1965).

Maintained by Alexander Pastukhov. Last updated 3 years ago.

11.5 match 4.00 score 20 scripts

dwarton

ecostats:Code and Data Accompanying the Eco-Stats Text (Warton 2022)

Functions and data supporting the Eco-Stats text (Warton, 2022, Springer), and solutions to exercises. Functions include tools for using simulation envelopes in diagnostic plots, and a function for diagnostic plots of multivariate linear models. Datasets mentioned in the package are included here (where not available elsewhere) and there is a vignette for each chapter of the text with solutions to exercises.

Maintained by David Warton. Last updated 1 years ago.

6.9 match 8 stars 6.58 score 53 scripts

s-fleck

lgr:A Fully Featured Logging Framework

A flexible, feature-rich yet light-weight logging framework based on 'R6' classes. It supports hierarchical loggers, custom log levels, arbitrary data fields in log events, logging to plaintext, 'JSON', (rotating) files, memory buffers. For extra appenders that support logging to databases, email and push notifications see the the package lgr.app.

Maintained by Stefan Fleck. Last updated 4 months ago.

log4j logging r6

4.0 match 81 stars 11.29 score 120 scripts 93 dependents

midasverse

rMIDAS:Multiple Imputation with Denoising Autoencoders

A tool for multiply imputing missing data using 'MIDAS', a deep learning method based on denoising autoencoder neural networks. This algorithm offers significant accuracy and efficiency advantages over other multiple imputation strategies, particularly when applied to large datasets with complex features. Alongside interfacing with 'Python' to run the core algorithm, this package contains functions for processing data before and after model training, running imputation model diagnostics, generating multiple completed datasets, and estimating regression models on these datasets.

Maintained by Thomas Robinson. Last updated 1 years ago.

deep-learning imputation-methods neural-network reticulate tensorflow

6.9 match 34 stars 6.53 score 33 scripts

eh-in-r

RCTS:Clustering Time Series While Resisting Outliers

Robust Clustering of Time Series (RCTS) has the functionality to cluster time series using both the classical and the robust interactive fixed effects framework. The classical framework is developed in Ando & Bai (2017) <doi:10.1080/01621459.2016.1195743>. The implementation within this package excludes the SCAD-penalty on the estimations of beta. This robust framework is developed in Boudt & Heyndels (2022) <doi:10.1016/j.ecosta.2022.01.002> and is made robust against different kinds of outliers. The algorithm iteratively updates beta (the coefficients of the observable variables), group membership, and the latent factors (which can be common and/or group-specific) along with their loadings. The number of groups and factors can be estimated if they are unknown.

Maintained by Ewoud Heyndels. Last updated 2 years ago.

22.4 match 2.00 score

cidm-ph

ggmapinset:Add Inset Panels to Maps

Helper to add insets based on geom_sf() from 'ggplot2'. This package gives you a drop-in replacement for geom_sf() that supports adding a zoomed inset map without having to create and embed a separate plot.

Maintained by Carl Suster. Last updated 3 months ago.

data-visualization geospatial ggplot-extension ggplot2

7.2 match 36 stars 6.21 score 9 scripts 1 dependents

tkonopka

umap:Uniform Manifold Approximation and Projection

Uniform manifold approximation and projection is a technique for dimension reduction. The algorithm was described by McInnes and Healy (2018) in <arXiv:1802.03426>. This package provides an interface for two implementations. One is written from scratch, including components for nearest-neighbor search and for embedding. The second implementation is a wrapper for 'python' package 'umap-learn' (requires separate installation, see vignette for more details).

Maintained by Tomasz Konopka. Last updated 11 months ago.

dimensionality-reduction umap cpp

3.5 match 132 stars 12.74 score 3.6k scripts 43 dependents

bioc

cardelino:Clone Identification from Single Cell Data

Methods to infer clonal tree configuration for a population of cells using single-cell RNA-seq data (scRNA-seq), and possibly other data modalities. Methods are also provided to assign cells to inferred clones and explore differences in gene expression between clones. These methods can flexibly integrate information from imperfect clonal trees inferred based on bulk exome-seq data, and sparse variant alleles expressed in scRNA-seq data. A flexible beta-binomial error model that accounts for stochastic dropout events as well as systematic allelic imbalance is used.

Maintained by Davis McCarthy. Last updated 5 months ago.

singlecell rnaseq visualization transcriptomics geneexpression sequencing software exomeseq clonal-clustering gibbs-sampling scrna-seq single-cell somatic-mutations

6.3 match 61 stars 7.05 score 62 scripts

geomorphr

geomorph:Geometric Morphometric Analyses of 2D and 3D Landmark Data

Read, manipulate, and digitize landmark data, generate shape variables via Procrustes analysis for points, curves and surfaces, perform shape analyses, and provide graphical depictions of shapes and patterns of shape variation.

Maintained by Dean Adams. Last updated 1 months ago.

3.7 match 76 stars 12.05 score 700 scripts 6 dependents

dgkf

testex:Add Tests to Examples

Add tests in-line in examples. Provides standalone functions for facilitating easier test writing in Rd files. However, a more familiar interface is provided using 'roxygen2' tags. Tools are also provided for facilitating package configuration and use with 'testthat'.

Maintained by Doug Kelkhoff. Last updated 11 months ago.

documentation examples rlang roxygen2 testing

7.2 match 23 stars 6.06 score 6 scripts

rstudio

blogdown:Create Blogs and Websites with R Markdown

Write blog posts and web pages in R Markdown. This package supports the static site generator 'Hugo' (<https://gohugo.io>) best, and it also supports 'Jekyll' (<https://jekyllrb.com>) and 'Hexo' (<https://hexo.io>).

Maintained by Yihui Xie. Last updated 1 days ago.

blog-engine blogdown hugo rmarkdown rstudio website-generation

3.8 match 1.8k stars 11.55 score 1.4k scripts 1 dependents

curso-r

auth0:Authentication in Shiny with Auth0

Uses Auth0 API (see <https://auth0.com> for more information) to use a simple authentication system. It provides tools to log in and out a shiny application using social networks or a list of e-mails.

Maintained by Julio Trecenti. Last updated 1 years ago.

auth0 authentication hacktoberfest shiny

5.5 match 156 stars 7.79 score 88 scripts

john-d-fox

Rcmdr:R Commander

A platform-independent basic-statistics GUI (graphical user interface) for R, based on the tcltk package.

Maintained by John Fox. Last updated 5 months ago.

4.5 match 4 stars 9.49 score 636 scripts 38 dependents

tidyverse

duckplyr:A 'DuckDB'-Backed Version of 'dplyr'

A drop-in replacement for 'dplyr', powered by 'DuckDB' for performance. Offers convenient utilities for working with in-memory and larger-than-memory data while retaining full 'dplyr' compatibility.

Maintained by Kirill Müller. Last updated 5 days ago.

analytics dataframe dplyr duckdb performance

3.8 match 309 stars 11.33 score 220 scripts

terminological

dtrackr:Track your Data Pipelines

Track and document 'dplyr' data pipelines. As you filter, mutate, and join your way through a data set, 'dtrackr' seamlessly keeps track of your data flow and makes publication ready documentation of a data pipeline simple.

Maintained by Robert Challen. Last updated 5 months ago.

4.8 match 69 stars 8.78 score 362 scripts 1 dependents

dreamrs

shinybusy:Busy Indicators and Notifications for 'Shiny' Applications

Add indicators (spinner, progress bar, gif) in your 'shiny' applications to show the user that the server is busy. And other tools to let your users know something is happening (send notifications, reports, ...).

Maintained by Victor Perrier. Last updated 6 months ago.

shiny

3.6 match 142 stars 11.70 score 772 scripts 39 dependents

pvermees

provenance:Statistical Toolbox for Sedimentary Provenance Analysis

Bundles a number of established statistical methods to facilitate the visual interpretation of large datasets in sedimentary geology. Includes functionality for adaptive kernel density estimation, principal component analysis, correspondence analysis, multidimensional scaling, generalised procrustes analysis and individual differences scaling using a variety of dissimilarity measures. Univariate provenance proxies, such as single-grain ages or (isotopic) compositions are compared with the Kolmogorov-Smirnov, Kuiper, Wasserstein-2 or Sircombe-Hazelton L2 distances. Categorical provenance proxies such as chemical compositions are compared with the Aitchison and Bray-Curtis distances,and count data with the chi-square distance. Varietal data can either be converted to one or more distributional datasets, or directly compared using the multivariate Wasserstein distance. Also included are tools to plot compositional and count data on ternary diagrams and point-counting data on radial plots, to calculate the sample size required for specified levels of statistical precision, and to assess the effects of hydraulic sorting on detrital compositions. Includes an intuitive query-based user interface for users who are not proficient in R.

Maintained by Pieter Vermeesch. Last updated 2 months ago.

7.6 match 14 stars 5.52 score 79 scripts 1 dependents

fishfollower

stockassessment:State-Space Assessment Model

Fitting SAM...

Maintained by Anders Nielsen. Last updated 14 days ago.

stockassessment cpp

5.4 match 49 stars 7.76 score 324 scripts 2 dependents

lorenzo125

EmiR:Evolutionary Minimizer for R

A C++ implementation of the following evolutionary algorithms: Bat Algorithm (Yang, 2010 <doi:10.1007/978-3-642-12538-6_6>), Cuckoo Search (Yang, 2009 <doi:10.1109/nabic.2009.5393690>), Genetic Algorithms (Holland, 1992, ISBN:978-0262581110), Gravitational Search Algorithm (Rashedi et al., 2009 <doi:10.1016/j.ins.2009.03.004>), Grey Wolf Optimization (Mirjalili et al., 2014 <doi:10.1016/j.advengsoft.2013.12.007>), Harmony Search (Geem et al., 2001 <doi:10.1177/003754970107600201>), Improved Harmony Search (Mahdavi et al., 2007 <doi:10.1016/j.amc.2006.11.033>), Moth-flame Optimization (Mirjalili, 2015 <doi:10.1016/j.knosys.2015.07.006>), Particle Swarm Optimization (Kennedy et al., 2001 ISBN:1558605959), Simulated Annealing (Kirkpatrick et al., 1983 <doi:10.1126/science.220.4598.671>), Whale Optimization Algorithm (Mirjalili and Lewis, 2016 <doi:10.1016/j.advengsoft.2016.01.008>). 'EmiR' can be used not only for unconstrained optimization problems, but also in presence of inequality constrains, and variables restricted to be integers.

Maintained by Lorenzo Sostero. Last updated 2 years ago.

cpp

23.6 match 1.74 score 11 scripts

bioc

iSEEu:iSEE Universe

iSEEu (the iSEE universe) contains diverse functionality to extend the usage of the iSEE package, including additional classes for the panels, or modes allowing easy configuration of iSEE applications.

Maintained by Kevin Rue-Albrecht. Last updated 5 months ago.

immunooncology visualization gui dimensionreduction featureextraction clustering transcription geneexpression transcriptomics singlecell cellbasedassays hacktoberfest

5.7 match 9 stars 7.15 score 35 scripts 1 dependents

paws-r

paws.common:Paws Low-Level Amazon Web Services API

Functions for making low-level API requests to Amazon Web Services <https://aws.amazon.com>. The functions handle building, signing, and sending requests, and receiving responses. They are designed to help build higher-level interfaces to individual services, such as Simple Storage Service (S3).

Maintained by Dyfan Jones. Last updated 4 days ago.

aws aws-sdk cpp

3.6 match 332 stars 11.07 score 39 dependents

briandconnelly

envvar:Make Working with Environment Variables Easier and More Consistent

A collection of functions that allows for easy and consistent use of environment variables. This includes setting, checking, retrieving, transforming, and validating values stored in environment variables.

Maintained by Brian Connelly. Last updated 7 months ago.

configuration environment-variables

10.0 match 17 stars 3.93 score 5 scripts

dyfanjones

sagemaker.common:R6sagemaker lower level api calls

`R6sagemaker` lower level api calls.

Maintained by Dyfan Jones. Last updated 3 years ago.

amazon-sagemaker aws sagemaker sdk

14.1 match 2.78 score 4 dependents

shikokuchuo

nanonext:NNG (Nanomsg Next Gen) Lightweight Messaging Library

R binding for NNG (Nanomsg Next Gen), a successor to ZeroMQ. NNG is a socket library for reliable, high-performance messaging over in-process, IPC, TCP, WebSocket and secure TLS transports. Implements 'Scalability Protocols', a standard for common communications patterns including publish/subscribe, request/reply and service discovery. As its own threaded concurrency framework, provides a toolkit for asynchronous programming and distributed computing. Intuitive 'aio' objects resolve automatically when asynchronous operations complete, and synchronisation primitives allow R to wait upon events signalled by concurrent threads.

Maintained by Charlie Gao. Last updated 2 days ago.

concurrency https ipc-message messaging-library nng rpc socket-communication synchronization-primitives tcp-protocol websocket mbedtls

4.0 match 60 stars 9.81 score 28 scripts 9 dependents

ropensci

magick:Advanced Graphics and Image-Processing in R

Bindings to 'ImageMagick': the most comprehensive open-source image processing library available. Supports many common formats (png, jpeg, tiff, pdf, etc) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All operations are vectorized via the Magick++ STL meaning they operate either on a single frame or a series of frames for working with layers, collages, or animation. In RStudio images are automatically previewed when printed to the console, resulting in an interactive editing environment. The latest version of the package includes a native graphics device for creating in-memory graphics or drawing onto images using pixel coordinates.

Maintained by Jeroen Ooms. Last updated 21 days ago.

image-manipulation image-processing imagemagick cpp

2.3 match 468 stars 17.31 score 9.0k scripts 256 dependents

cloudyr

googleComputeEngineR:R Interface with Google Compute Engine

Interact with the 'Google Compute Engine' API in R. Lets you create, start and stop instances in the 'Google Cloud'. Support for preconfigured instances, with templates for common R needs.

Maintained by Mark Edmondson. Last updated 2 days ago.

api cloud-computing cloudyr google-cloud googleauthr launching-virtual-machines

3.9 match 152 stars 9.73 score 235 scripts

hypertidy

vapour:Access to the 'Geospatial Data Abstraction Library' ('GDAL')

Provides low-level access to 'GDAL' functionality. 'GDAL' is the 'Geospatial Data Abstraction Library' a translator for raster and vector geospatial data formats that presents a single raster abstract data model and single vector abstract data model to the calling application for all supported formats <https://gdal.org/>. This package is focussed on providing exactly and only what GDAL does, to enable developing further tools.

Maintained by Michael Sumner. Last updated 9 months ago.

cpp gdal gdal-api cpp

4.1 match 86 stars 9.31 score 63 scripts 5 dependents

yaoxiangli

rconf:Minimal and Lightweight Configuration Tool

Minimal and lightweight configuration tool that provides basic support for 'YAML' configuration files without requiring additional package dependencies. It offers a simple method for loading and parsing configuration settings, making it ideal for quick prototypes and lightweight projects.

Maintained by Yaoxiang Li. Last updated 14 days ago.

14.1 match 2.70 score

tymekdev

fig:A Config Package with No "Con"

Work with configs with a source precedence. Either create own R6 instance or work with convenient functions at a package level.

Maintained by Tymoteusz Makowski. Last updated 3 years ago.

configuration

11.9 match 3 stars 3.18 score 1 scripts

ropensci

ruODK:An R Client for the ODK Central API

Access and tidy up data from the 'ODK Central' API. 'ODK Central' is a clearinghouse for digitally captured data using ODK <https://docs.getodk.org/central-intro/>. It manages user accounts and permissions, stores form definitions, and allows data collection clients like 'ODK Collect' to connect to it for form download and submission upload. The 'ODK Central' API is documented at <https://docs.getodk.org/central-api/>.

Maintained by Florian W. Mayer. Last updated 4 months ago.

database open-data odk api data dataset odata odata-client odk-central opendatakit

4.9 match 42 stars 7.73 score 57 scripts 1 dependents

damurka

khisr:An R Client to Retrieve Data from DHIS2

Provides a user-friendly interface for interacting with the District Health Information Software 2 (DHIS2) instance. It streamlines data retrieval, empowering researchers, analysts, and healthcare professionals to obtain and utilize data efficiently.

Maintained by David Kariuki. Last updated 5 months ago.

dhis2 khis

7.9 match 1 stars 4.78 score 7 scripts 1 dependents

ropensci

babelquarto:Renders a Multilingual Quarto Book

Automate rendering and cross-linking of Quarto books following a prescribed structure.

Maintained by Maëlle Salmon. Last updated 1 months ago.

5.0 match 43 stars 7.52 score 23 scripts 1 dependents

jiefei-wang

aws.ecx:Communicating with AWS EC2 and ECS using AWS REST APIs

Providing the functions for communicating with Amazon Web Services(AWS) Elastic Compute Cloud(EC2) and Elastic Container Service(ECS). The functions will have the prefix 'ecs_' or 'ec2_' depending on the class of the API. The request will be sent via the REST API and the parameters are given by the function argument. The credentials can be set via 'aws_set_credentials'. The EC2 documentation can be found at <https://docs.aws.amazon.com/AWSEC2/latest/APIReference/Welcome.html> and ECS can be found at <https://docs.aws.amazon.com/AmazonECS/latest/APIReference/Welcome.html>.

Maintained by Jiefei Wang. Last updated 3 years ago.

ec2 ecs ecs-functions

9.0 match 1 stars 4.18 score 2 scripts

thinkr-open

fusen:Build a Package from Rmarkdown Files

Use Rmarkdown First method to build your package. Start your package with documentation, functions, examples and tests in the same unique file. Everything can be set from the Rmarkdown template file provided in your project, then inflated as a package. Inflating the template copies the relevant chunks and sections in the appropriate files required for package development.

Maintained by Vincent Guyader. Last updated 2 months ago.

hacktoberfest rmd-first

4.0 match 163 stars 9.45 score 35 scripts

workflowr

workflowr:A Framework for Reproducible and Collaborative Data Science

Provides a workflow for your analysis projects by combining literate programming ('knitr' and 'rmarkdown') and version control ('Git', via 'git2r') to generate a website containing time-stamped, versioned, and documented results.

Maintained by John Blischak. Last updated 4 months ago.

git project-management rmarkdown website workflow

3.1 match 845 stars 11.83 score 566 scripts

rstudio

rmarkdown:Dynamic Documents for R

Convert R Markdown documents into a variety of formats.

Maintained by Yihui Xie. Last updated 4 months ago.

literate-programming markdown pandoc rmarkdown

1.7 match 2.9k stars 21.79 score 14k scripts 3.7k dependents

cran

BAMMtools:Analysis and Visualization of Macroevolutionary Dynamics on Phylogenetic Trees

Provides functions for analyzing and visualizing complex macroevolutionary dynamics on phylogenetic trees. It is a companion package to the command line program BAMM (Bayesian Analysis of Macroevolutionary Mixtures) and is entirely oriented towards the analysis, interpretation, and visualization of evolutionary rates. Functionality includes visualization of rate shifts on phylogenies, estimating evolutionary rates through time, comparing posterior distributions of evolutionary rates across clades, comparing diversification models using Bayes factors, and more.

Maintained by Pascal Title. Last updated 6 months ago.

12.1 match 3.03 score 2 dependents

bioc

OmnipathR:OmniPath web service client and more

A client for the OmniPath web service (https://www.omnipathdb.org) and many other resources. It also includes functions to transform and pretty print some of the downloaded data, functions to access a number of other resources such as BioPlex, ConsensusPathDB, EVEX, Gene Ontology, Guide to Pharmacology (IUPHAR/BPS), Harmonizome, HTRIdb, Human Phenotype Ontology, InWeb InBioMap, KEGG Pathway, Pathway Commons, Ramilowski et al. 2015, RegNetwork, ReMap, TF census, TRRUST and Vinayagam et al. 2011. Furthermore, OmnipathR features a close integration with the NicheNet method for ligand activity prediction from transcriptomics data, and its R implementation `nichenetr` (available only on github).

Maintained by Denes Turei. Last updated 19 days ago.

graphandnetwork network pathways software thirdpartyclient dataimport datarepresentation genesignaling generegulation systemsbiology transcriptomics singlecell annotation kegg complexes enzyme-ptm networks networks-biology omnipath proteins quarto

3.7 match 126 stars 9.90 score 226 scripts 2 dependents

milesmcbain

datapasta:R Tools for Data Copy-Pasta

RStudio addins and R functions that make copy-pasting vectors and tables to text painless.

Maintained by Miles McBain. Last updated 3 years ago.

addin clipboard copypaste excel tibble

3.5 match 899 stars 10.32 score 290 scripts 2 dependents

strand-tech

strand:A Framework for Investment Strategy Simulation

Provides a framework for performing discrete (share-level) simulations of investment strategies. Simulated portfolios optimize exposure to an input signal subject to constraints such as position size and factor exposure. For background see L. Chincarini and D. Kim (2010, ISBN:978-0-07-145939-6) "Quantitative Equity Portfolio Management".

Maintained by Jeff Enos. Last updated 4 years ago.

5.9 match 24 stars 6.14 score 38 scripts

jeroen

openssl:Toolkit for Encryption, Signatures and Certificates Based on OpenSSL

Bindings to OpenSSL libssl and libcrypto, plus custom SSH key parsers. Supports RSA, DSA and EC curves P-256, P-384, P-521, and curve25519. Cryptographic signatures can either be created and verified manually or via x509 certificates. AES can be used in cbc, ctr or gcm mode for symmetric encryption; RSA for asymmetric (public key) encryption or EC for Diffie Hellman. High-level envelope functions combine RSA and AES for encrypting arbitrary sized data. Other utilities include key generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure random number generator, and 'bignum' math methods for manually performing crypto calculations on large multibyte integers.

Maintained by Jeroen Ooms. Last updated 1 months ago.

openssl

2.0 match 65 stars 18.00 score 632 scripts 5.0k dependents

kwb-r

kwb.monitoring:Functions Used Within Different Kwb Monitoring Projects

Functions used within different KWB projects dealing with monitoring data.

Maintained by Hauke Sonnenberg. Last updated 6 years ago.

monitoring

9.5 match 3.78 score 3 scripts 4 dependents

phiala

ecodist:Dissimilarity-Based Functions for Ecological Analysis

Dissimilarity-based analysis functions including ordination and Mantel test functions, intended for use with spatial and community ecological data. The original package description is in Goslee and Urban (2007) <doi:10.18637/jss.v022.i07>, with further statistical detail in Goslee (2010) <doi:10.1007/s11258-009-9641-0>.

Maintained by Sarah Goslee. Last updated 1 years ago.

openblas

3.6 match 9 stars 9.84 score 566 scripts 9 dependents

e-sensing

sits:Satellite Image Time Series Analysis for Earth Observation Data Cubes

An end-to-end toolkit for land use and land cover classification using big Earth observation data, based on machine learning methods applied to satellite image data cubes, as described in Simoes et al (2021) <doi:10.3390/rs13132428>. Builds regular data cubes from collections in AWS, Microsoft Planetary Computer, Brazil Data Cube, Copernicus Data Space Environment (CDSE), Digital Earth Africa, Digital Earth Australia, NASA HLS using the Spatio-temporal Asset Catalog (STAC) protocol (<https://stacspec.org/>) and the 'gdalcubes' R package developed by Appel and Pebesma (2019) <doi:10.3390/data4030092>. Supports visualization methods for images and time series and smoothing filters for dealing with noisy time series. Includes functions for quality assessment of training samples using self-organized maps as presented by Santos et al (2021) <doi:10.1016/j.isprsjprs.2021.04.014>. Includes methods to reduce training samples imbalance proposed by Chawla et al (2002) <doi:10.1613/jair.953>. Provides machine learning methods including support vector machines, random forests, extreme gradient boosting, multi-layer perceptrons, temporal convolutional neural networks proposed by Pelletier et al (2019) <doi:10.3390/rs11050523>, and temporal attention encoders by Garnot and Landrieu (2020) <doi:10.48550/arXiv.2007.00586>. Supports GPU processing of deep learning models using torch <https://torch.mlverse.org/>. Performs efficient classification of big Earth observation data cubes and includes functions for post-classification smoothing based on Bayesian inference as described by Camara et al (2024) <doi:10.3390/rs16234572>, and methods for active learning and uncertainty assessment. Supports region-based time series analysis using package supercells <https://jakubnowosad.com/supercells/>. Enables best practices for estimating area and assessing accuracy of land change as recommended by Olofsson et al (2014) <doi:10.1016/j.rse.2014.02.015>. Minimum recommended requirements: 16 GB RAM and 4 CPU dual-core.

Maintained by Gilberto Camara. Last updated 1 months ago.

big-earth-data cbers earth-observation eo-datacubes geospatial image-time-series land-cover-classification landsat planetary-computer r-spatial remote-sensing rspatial satellite-image-time-series satellite-imagery sentinel-2 stac-api stac-catalog cpp

3.8 match 494 stars 9.50 score 384 scripts

rstudio

rstudioapi:Safely Access the RStudio API

Access the RStudio API (if available) and provide informative error messages when it's not.

Maintained by Kevin Ushey. Last updated 4 months ago.

1.9 match 172 stars 18.81 score 3.6k scripts 2.1k dependents

kpagacz

tergo:Style Your Code Fast

Provides a set of functions that allow users for styling their R code according to the 'tidyverse' style guide. The package uses a native Rust implementation to ensure the highest performance. Learn more about 'tergo' at <https://rtergo.pagacz.io>.

Maintained by Konrad Pagacz. Last updated 30 days ago.

rust cargo

6.3 match 36 stars 5.56 score 3 scripts

r-dbi

RSQLite:SQLite Interface for R

Embeds the SQLite database engine in R and provides an interface compliant with the DBI package. The source for the SQLite engine and for various extensions in a recent version is included. System libraries will never be consulted because this package relies on static linking for the plugins it includes; this also ensures a consistent experience across all installations.

Maintained by Kirill Müller. Last updated 25 days ago.

database sqlite3 cpp

1.9 match 327 stars 18.73 score 8.1k scripts 1.1k dependents

vegandevs

vegan:Community Ecology Package

Ordination methods, diversity analysis and other functions for community and vegetation ecologists.

Maintained by Jari Oksanen. Last updated 17 days ago.

ecological-modelling ecology ordination fortran openblas

1.8 match 472 stars 19.41 score 15k scripts 440 dependents

insightsengineering

sasr:'SAS' Interface

Provides a 'SAS' interface, through 'SASPy'(<https://sassoftware.github.io/saspy/>) and 'reticulate'(<https://rstudio.github.io/reticulate/>). This package helps you create 'SAS' sessions, execute 'SAS' code in remote 'SAS' servers, retrieve execution results and log, and exchange datasets between 'SAS' and 'R'. It also helps you to install 'SASPy' and create a configuration file for the connection. Please review the 'SASPy' license file as instructed so that you comply with its separate and independent license.

Maintained by Liming Li. Last updated 2 years ago.

statistical-engineering

5.9 match 15 stars 5.90 score 21 scripts

pmair78

smacof:Multidimensional Scaling

Implements the following approaches for multidimensional scaling (MDS) based on stress minimization using majorization (smacof): ratio/interval/ordinal/spline MDS on symmetric dissimilarity matrices, MDS with external constraints on the configuration, individual differences scaling (idioscal, indscal), MDS with spherical restrictions, and ratio/interval/ordinal/spline unfolding (circular restrictions, row-conditional). Various tools and extensions like jackknife MDS, bootstrap MDS, permutation tests, MDS biplots, gravity models, unidimensional scaling, drift vectors (asymmetric MDS), classical scaling, and Procrustes are implemented as well.

Maintained by Patrick Mair. Last updated 5 months ago.

4.4 match 5 stars 7.86 score 152 scripts 24 dependents

dreamrs

apexcharter:Create Interactive Chart with the JavaScript 'ApexCharts' Library

Provides an 'htmlwidgets' interface to 'apexcharts.js'. 'Apexcharts' is a modern JavaScript charting library to build interactive charts and visualizations with simple API. 'Apexcharts' examples and documentation are available here: <https://apexcharts.com/>.

Maintained by Victor Perrier. Last updated 26 days ago.

data-visualization htmlwidgets

4.0 match 144 stars 8.51 score 247 scripts

ropensci

beautier:'BEAUti' from R

'BEAST2' (<https://www.beast2.org>) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'BEAUti 2' (which is part of 'BEAST2') is a GUI tool that allows users to specify the many possible setups and generates the XML file 'BEAST2' needs to run. This package provides a way to create 'BEAST2' input files without active user input, but using R function calls instead.

Maintained by Richèl J.C. Bilderbeek. Last updated 23 days ago.

bayesian beast beast2 beauti phylogenetic-inference phylogenetics

3.9 match 13 stars 8.76 score 198 scripts 5 dependents

hegghammer

daiR:Interface with Google Cloud Document AI API

R interface for the Google Cloud Services 'Document AI API' <https://cloud.google.com/document-ai/> with additional tools for output file parsing and text reconstruction. 'Document AI' is a powerful server-based OCR service that extracts text and tables from images and PDF files with high accuracy. 'daiR' gives R users programmatic access to this service and additional tools to handle and visualize the output. See the package website <https://dair.info/> for more information and examples.

Maintained by Thomas Hegghammer. Last updated 4 months ago.

google-cloud ocr

5.0 match 42 stars 6.77 score 40 scripts

bioc

EnrichmentBrowser:Seamless navigation through combined results of set-based and network-based enrichment analysis

The EnrichmentBrowser package implements essential functionality for the enrichment analysis of gene expression data. The analysis combines the advantages of set-based and network-based enrichment analysis in order to derive high-confidence gene sets and biological pathways that are differentially regulated in the expression data under investigation. Besides, the package facilitates the visualization and exploration of such sets and pathways.

Maintained by Ludwig Geistlinger. Last updated 5 months ago.

immunooncology microarray rnaseq geneexpression differentialexpression pathways graphandnetwork network genesetenrichment networkenrichment visualization reportwriting

3.6 match 20 stars 9.37 score 164 scripts 3 dependents

rstudio

rsconnect:Deploy Docs, Apps, and APIs to 'Posit Connect', 'shinyapps.io', and 'RPubs'

Programmatic deployment interface for 'RPubs', 'shinyapps.io', and 'Posit Connect'. Supported content types include R Markdown documents, Shiny applications, Plumber APIs, plots, and static web content.

Maintained by Aron Atkins. Last updated 16 days ago.

2.3 match 139 stars 14.90 score 3.1k scripts 6 dependents

gofigr

gofigR:Client for 'GoFigr.io'

Integrates with your 'RMarkdown' documents to automatically publish figures to the <https://GoFigr.io> service. Supports both 'knitr' and interactive execution within 'RStudio'.

Maintained by Maciej Pacula. Last updated 2 days ago.

9.9 match 3.40 score

ropensci

nlrx:Setup, Run and Analyze 'NetLogo' Model Simulations from 'R' via 'XML'

Setup, run and analyze 'NetLogo' (<https://ccl.northwestern.edu/netlogo/>) model simulations in 'R'. 'nlrx' experiments use a similar structure as 'NetLogos' Behavior Space experiments. However, 'nlrx' offers more flexibility and additional tools for running and analyzing complex simulation designs and sensitivity analyses. The user defines all information that is needed in an intuitive framework, using class objects. Experiments are submitted from 'R' to 'NetLogo' via 'XML' files that are dynamically written, based on specifications defined by the user. By nesting model calls in future environments, large simulation design with many runs can be executed in parallel. This also enables simulating 'NetLogo' experiments on remote high performance computing machines. In order to use this package, 'Java' and 'NetLogo' (>= 5.3.1) need to be available on the executing system.

Maintained by Sebastian Hanss. Last updated 6 months ago.

agent-based-modeling individual-based-modelling netlogo peer-reviewed

3.8 match 78 stars 8.86 score 195 scripts

john-harrold

formods:'Shiny' Modules for General Tasks

'Shiny' apps can often make use of the same key elements, this package provides modules for common tasks (data upload, wrangling data, figure generation and saving the app state), and also a framework for developing. These modules can react and interact as well as generate code to create reproducible analyses.

Maintained by John Harrold. Last updated 7 days ago.

4.2 match 8 stars 7.94 score 100 scripts 1 dependents

claudiozandonella

trackdown:Collaborative Editing of Rmd (or Quarto / Rnw) Documents in Google Drive

Collaborative writing and editing of R Markdown (or Quarto / Sweave) documents. The local .Rmd (or Quarto / .Rnw) is uploaded as a plain-text file to Google Drive. By taking advantage of the easily readable Markdown (or LaTeX) syntax and the well-known online interface offered by Google Docs, collaborators can easily contribute to the writing and editing process. After integrating all authors’ contributions, the final document can be downloaded and rendered locally.

Maintained by Claudio Zandonella Callegher. Last updated 2 years ago.

markdown reproducible-research

3.9 match 219 stars 8.48 score 69 scripts

r-lib

sessioninfo:R Session Information

Query and print information about the current R session. It is similar to 'utils::sessionInfo()', but includes more information about packages, and where they were installed from.

Maintained by Gábor Csárdi. Last updated 1 months ago.

2.3 match 76 stars 14.57 score 4.3k scripts 237 dependents

pecanproject

PEcAn.MAAT:PEcAn Package for Integration of the MAAT Model

This module provides functions to wrap the MAAT model into the PEcAn workflows.

Maintained by Shawn Serbin. Last updated 3 days ago.

bayesian cyberinfrastructure data-assimilation data-science ecosystem-model ecosystem-science forecasting meta-analysis national-science-foundation pecan plants

3.6 match 216 stars 8.94 score 12 scripts

davidgohel

flextable:Functions for Tabular Reporting

Use a grammar for creating and customizing pretty tables. The following formats are supported: 'HTML', 'PDF', 'RTF', 'Microsoft Word', 'Microsoft PowerPoint' and R 'Grid Graphics'. 'R Markdown', 'Quarto' and the package 'officer' can be used to produce the result files. The syntax is the same for the user regardless of the type of output to be produced. A set of functions allows the creation, definition of cell arrangement, addition of headers or footers, formatting and definition of cell content with text and or images. The package also offers a set of high-level functions that allow tabular reporting of statistical models and the creation of complex cross tabulations.

Maintained by David Gohel. Last updated 1 months ago.

docx html5 ms-office-documents rmarkdown table

1.9 match 583 stars 17.04 score 7.3k scripts 119 dependents

usepa

tcpl:ToxCast Data Analysis Pipeline

The ToxCast Data Analysis Pipeline ('tcpl') is an R package that manages, curve-fits, plots, and stores ToxCast data to populate its linked MySQL database, 'invitrodb'. The package was developed for the chemical screening data curated by the US EPA's Toxicity Forecaster (ToxCast) program, but 'tcpl' can be used to support diverse chemical screening efforts.

Maintained by Jason Brown. Last updated 3 days ago.

ccte comptox ord

3.4 match 36 stars 9.41 score 90 scripts

jbkunst

highcharter:A Wrapper for the 'Highcharts' Library

A wrapper for the 'Highcharts' library including shortcut functions to plot R objects. 'Highcharts' <https://www.highcharts.com/> is a charting library offering numerous chart types with a simple configuration syntax.

Maintained by Joshua Kunst. Last updated 1 years ago.

highcharts htmlwidgets shiny shiny-r visualization wrapper

2.3 match 725 stars 13.93 score 4.9k scripts 18 dependents

r-lib

generics:Common S3 Generics not Provided by Base R Methods Related to Model Fitting

In order to reduce potential package dependencies and conflicts, generics provides a number of commonly used S3 generics.

Maintained by Hadley Wickham. Last updated 1 years ago.

2.3 match 61 stars 14.00 score 131 scripts 9.8k dependents

cran

binGroup:Evaluation and Experimental Design for Binomial Group Testing

Methods for estimation and hypothesis testing of proportions in group testing designs: methods for estimating a proportion in a single population (assuming sensitivity and specificity equal to 1 in designs with equal group sizes), as well as hypothesis tests and functions for experimental design for this situation. For estimating one proportion or the difference of proportions, a number of confidence interval methods are included, which can deal with various different pool sizes. Further, regression methods are implemented for simple pooling and matrix pooling designs. Methods for identification of positive items in group testing designs: Optimal testing configurations can be found for hierarchical and array-based algorithms. Operating characteristics can be calculated for testing configurations across a wide variety of situations.

Maintained by Frank Schaarschmidt. Last updated 7 years ago.

14.2 match 2.18 score

poissonconsulting

batchr:Batch Process Files

Processes multiple files with a user-supplied function. The key design principle is that only files which were last modified before the directory was configured are processed. A hidden file stores the configuration time and function etc while successfully processed files are automatically touched to update their modification date. As a result batch processing can be stopped and restarted and any files created (or modified or deleted) during processing are ignored.

Maintained by Joe Thorley. Last updated 2 months ago.

batch-processing

6.8 match 6 stars 4.56 score 8 scripts

andodet

googlePubsubR:R Interface for Google 'Cloud Pub/Sub' REST API

Provides an easy to use interface to the 'Google Pub/Sub' REST API <https://cloud.google.com/pubsub/docs/reference/rest>.

Maintained by Andrea Dodet. Last updated 2 years ago.

api-client google-pubsub

5.8 match 10 stars 5.34 score 22 scripts

ralmond

RNetica:R interface to Netica(R) Bayesian Network Engine

This provides an R interface to the Netica (http://norsys.com/) Bayesian network library API.

Maintained by Russell Almond. Last updated 2 months ago.

bayesian-network

6.2 match 2 stars 4.92 score 14 scripts 2 dependents

bioc

biodb:biodb, a library and a development framework for connecting to chemical and biological databases

The biodb package provides access to standard remote chemical and biological databases (ChEBI, KEGG, HMDB, ...), as well as to in-house local database files (CSV, SQLite), with easy retrieval of entries, access to web services, search of compounds by mass and/or name, and mass spectra matching for LCMS and MSMS. Its architecture as a development framework facilitates the development of new database connectors for local projects or inside separate published packages.

Maintained by Pierrick Roger. Last updated 5 months ago.

software infrastructure dataimport kegg biology cheminformatics chemistry databases cpp

3.9 match 11 stars 7.85 score 24 scripts 6 dependents

civisanalytics

civis:R Client for the 'Civis Platform API'

A convenient interface for making requests directly to the 'Civis Platform API' <https://www.civisanalytics.com/platform/>. Full documentation available 'here' <https://civisanalytics.github.io/civis-r/>.

Maintained by Peter Cooman. Last updated 2 months ago.

3.9 match 16 stars 7.84 score 144 scripts

techtonique

bcn:Boosted Configuration Networks

Boosted Configuration (neural) Networks for supervised learning.

Maintained by T. Moudiki. Last updated 6 months ago.

machine-learning neural-networks statistical-learning cpp

7.5 match 5 stars 4.00 score 4 scripts

pecanproject

PEcAn.workflow:PEcAn Functions Used for Ecological Forecasts and Reanalysis

The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The goal of PEcAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation. This package provides workhorse functions that can be used to run the major steps of a PEcAn analysis.

Maintained by David LeBauer. Last updated 3 days ago.

bayesian cyberinfrastructure data-assimilation data-science ecosystem-model ecosystem-science forecasting meta-analysis national-science-foundation pecan plants jags cpp

3.4 match 216 stars 8.82 score 15 scripts 4 dependents

hubverse-org

hubUtils:Core 'hubverse' Utilities

Core set of low-level utilities common across the 'hubverse'. Used to interact with 'hubverse' schema, Hub configuration files and model outputs and designed to be primarily used internally by other 'hubverse' packages. See Reich et al. (2022) <doi:10.2105/AJPH.2022.306831> for an overview of Collaborative Hubs.

Maintained by Anna Krystalli. Last updated 5 days ago.

hubverse

4.1 match 6 stars 7.22 score 49 scripts 7 dependents

luomus

fbi:Finnish Biodiversity Indicators

Finnish biodiversity indicators is a service providing time series of abundance indices and related metrics for Finland. The input data for the indices are provided by the Finnish Biodiversity Information Facility.

Maintained by William K. Morris. Last updated 3 days ago.

5.0 match 5.89 score 60 scripts

tconwell

bsTools:Create HTML Content with Bootstrap 5 Classes and Layouts

Functions are pre-configured to utilize Bootstrap 5 classes and HTML structures to create Bootstrap-styled HTML quickly and easily. Includes functions for creating common Bootstrap elements such as containers, rows, cols, navbars, etc. Intended to be used with the html5 package. Learn more at <https://getbootstrap.com/>.

Maintained by Timothy Conwell. Last updated 2 years ago.

10.8 match 1 stars 2.70 score 2 scripts

marcohlmann

metanetwork:Handling and Representing Trophic Networks in Space and Time

A toolbox to handle and represent trophic networks in space or time across aggregation levels. This package contains a layout algorithm specifically designed for trophic networks, using dimension reduction on a diffusion graph kernel and trophic levels. Importantly, this package provides a layout method applicable for large trophic networks. The package also implements network diversity indices at different aggregation levels and connectance computation.

Maintained by Marc Ohlmann. Last updated 2 years ago.

7.5 match 2 stars 3.89 score 77 scripts

bioc

AneuFinder:Analysis of Copy Number Variation in Single-Cell-Sequencing Data

AneuFinder implements functions for copy-number detection, breakpoint detection, and karyotype and heterogeneity analysis in single-cell whole genome sequencing and strand-seq data.

Maintained by Aaron Taudt. Last updated 5 months ago.

immunooncology software sequencing singlecell copynumbervariation genomicvariation hiddenmarkovmodel wholegenome cpp

3.8 match 17 stars 7.70 score 37 scripts

bioc

sRACIPE:Systems biology tool to simulate gene regulatory circuits

sRACIPE implements a randomization-based method for gene circuit modeling. It allows us to study the effect of both the gene expression noise and the parametric variation on any gene regulatory circuit (GRC) using only its topology, and simulates an ensemble of models with random kinetic parameters at multiple noise levels. Statistical analysis of the generated gene expressions reveals the basin of attraction and stability of various phenotypic states and their changes associated with intrinsic and extrinsic noises. sRACIPE provides a holistic picture to evaluate the effects of both the stochastic nature of cellular processes and the parametric variation.

Maintained by Mingyang Lu. Last updated 20 days ago.

researchfield systemsbiology mathematicalbiology geneexpression generegulation genetarget cpp

4.5 match 4 stars 6.40 score 209 scripts

leondap

recluster:Ordination Methods for the Analysis of Beta-Diversity Indices

The analysis of different aspects of biodiversity requires specific algorithms. For example, in regionalisation analyses, the high frequency of ties and zero values in dissimilarity matrices produced by Beta-diversity turnover produces hierarchical cluster dendrograms whose topology and bootstrap supports are affected by the order of rows in the original matrix. Moreover, visualisation of biogeographical regionalisation can be facilitated by a combination of hierarchical clustering and multi-dimensional scaling. The recluster package provides robust techniques to visualise and analyse pattern of biodiversity and to improve occurrence data for cryptic taxa.

Maintained by Leonardo Dapporto. Last updated 4 months ago.

6.1 match 4 stars 4.69 score 41 scripts

dyfanjones

noctua:Connect to 'AWS Athena' using R 'AWS SDK' 'paws' ('DBI' Interface)

Designed to be compatible with the 'R' package 'DBI' (Database Interface) when connecting to Amazon Web Service ('AWS') Athena <https://aws.amazon.com/athena/>. To do this the 'R' 'AWS' Software Development Kit ('SDK') 'paws' <https://github.com/paws-r/paws> is used as a driver.

Maintained by Dyfan Jones. Last updated 11 months ago.

athena aws database

3.8 match 46 stars 7.48 score 58 scripts

carpentries

sandpaper:Create and Curate Carpentries Lessons

We provide tools to build a Carpentries-themed lesson repository into an accessible standalone static website. These include local tools and those designed to be used in a continuous integration context so that all the lesson author needs to focus on is writing the content of the actual lesson.

Maintained by Robert Davey. Last updated 2 months ago.

carpentries carpentries-infrastructure carpentries-workbench lesson-template lessons markdown static-site-generator

3.7 match 44 stars 7.72 score 8 scripts

elilillyco

rfacts:R Interface to 'FACTS' on Unix-Like Systems

The 'rfacts' package is an R interface to the Fixed and Adaptive Clinical Trial Simulator ('FACTS') on Unix-like systems. It programmatically invokes 'FACTS' to run clinical trial simulations, and it aggregates simulation output data into tidy data frames. These capabilities provide end-to-end automation for large-scale simulation pipelines, and they enhance computational reproducibility. For more information on 'FACTS' itself, please visit <https://www.berryconsultants.com/software/>.

Maintained by William Michael Landau. Last updated 3 years ago.

clinical-trials facts simulation

5.6 match 7 stars 5.02 score 10 scripts

yihui

servr:A Simple HTTP Server to Serve Static Files or Dynamic Documents

Start an HTTP server in R to serve static files, or dynamic documents that can be converted to HTML files (e.g., R Markdown) under a given directory.

Maintained by Yihui Xie. Last updated 2 months ago.

http-server web-server websocket

2.3 match 283 stars 12.51 score 190 scripts 94 dependents

dreamrs

vchartr:Interactive Charts with the 'JavaScript' 'VChart' Library

Provides an 'htmlwidgets' interface to 'VChart.js'. 'VChart', more than just a cross-platform charting library, but also an expressive data storyteller. 'VChart' examples and documentation are available here: <https://www.visactor.io/vchart>.

Maintained by Victor Perrier. Last updated 2 months ago.

4.0 match 9 stars 6.89 score 96 scripts

rstudio

renv:Project Environments

A dependency management toolkit for R. Using 'renv', you can create and manage project-local R libraries, save the state of these libraries to a 'lockfile', and later restore your library as required. Together, these tools can help make your projects more isolated, portable, and reproducible.

Maintained by Kevin Ushey. Last updated 4 days ago.

1.5 match 1.0k stars 18.55 score 1.5k scripts 113 dependents

r-lib

rcmdcheck:Run 'R CMD check' from 'R' and Capture Results

Run 'R CMD check' from 'R' and capture the results of the individual checks. Supports running checks in the background, timeouts, pretty printing and comparing check results.

Maintained by Gábor Csárdi. Last updated 5 months ago.

2.3 match 116 stars 12.34 score 102 scripts 158 dependents

bioc

Biobase:Biobase: Base functions for Bioconductor

Functions that are needed by many other packages or which replace R functions.

Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.

infrastructure bioconductor-package core-package

1.7 match 9 stars 16.45 score 6.6k scripts 1.8k dependents

r-lib

pkgdown:Make Static HTML Documentation for a Package

Generate an attractive and useful website from a source package. 'pkgdown' converts your documentation, vignettes, 'README', and more to 'HTML' making it easy to share information about your package online.

Maintained by Hadley Wickham. Last updated 17 hours ago.

documentation-tool

1.5 match 734 stars 18.47 score 588 scripts 162 dependents

gi0na

ghypernet:Fit and Simulate Generalised Hypergeometric Ensembles of Graphs

Provides functions for model fitting and selection of generalised hypergeometric ensembles of random graphs (gHypEG). To learn how to use it, check the vignettes for a quick tutorial. Please reference its use as Casiraghi, G., Nanumyan, V. (2019) <doi:10.5281/zenodo.2555300> together with those relevant references from the one listed below. The package is based on the research developed at the Chair of Systems Design, ETH Zurich. Casiraghi, G., Nanumyan, V., Scholtes, I., Schweitzer, F. (2016) <arXiv:1607.02441>. Casiraghi, G., Nanumyan, V., Scholtes, I., Schweitzer, F. (2017) <doi:10.1007/978-3-319-67256-4_11>. Casiraghi, G., (2017) <arXiv:1702.02048> Brandenberger, L., Casiraghi, G., Nanumyan, V., Schweitzer, F. (2019) <doi:10.1145/3341161.3342926> Casiraghi, G. (2019) <doi:10.1007/s41109-019-0241-1>. Casiraghi, G., Nanumyan, V. (2021) <doi:10.1038/s41598-021-92519-y>. Casiraghi, G. (2021) <doi:10.1088/2632-072X/ac0493>.

Maintained by Giona Casiraghi. Last updated 11 months ago.

data-mining data-science graphs network network-analysis random-graph-generation random-graphs

4.9 match 8 stars 5.68 score 20 scripts

distancedevelopment

mrds:Mark-Recapture Distance Sampling

Animal abundance estimation via conventional, multiple covariate and mark-recapture distance sampling (CDS/MCDS/MRDS). Detection function fitting is performed via maximum likelihood. Also included are diagnostics and plotting for fitted detection functions. Abundance estimation is via a Horvitz-Thompson-like estimator.

Maintained by Laura Marshall. Last updated 2 months ago.

3.4 match 4 stars 8.05 score 78 scripts 7 dependents

rstudio

tensorflow:R Interface to 'TensorFlow'

Interface to 'TensorFlow' <https://www.tensorflow.org/>, an open source software library for numerical computation using data flow graphs. Nodes in the graph represent mathematical operations, while the graph edges represent the multidimensional data arrays (tensors) communicated between them. The flexible architecture allows you to deploy computation to one or more 'CPUs' or 'GPUs' in a desktop, server, or mobile device with a single 'API'. 'TensorFlow' was originally developed by researchers and engineers working on the Google Brain Team within Google's Machine Intelligence research organization for the purposes of conducting machine learning and deep neural networks research, but the system is general enough to be applicable in a wide variety of other domains as well.

Maintained by Tomasz Kalinowski. Last updated 16 days ago.

1.8 match 1.3k stars 15.35 score 3.2k scripts 74 dependents

stochastictree

stochtree:Stochastic Tree Ensembles (XBART and BART) for Supervised Learning and Causal Inference

Flexible stochastic tree ensemble software. Robust implementations of Bayesian Additive Regression Trees (BART) Chipman, George, McCulloch (2010) <doi:10.1214/09-AOAS285> for supervised learning and Bayesian Causal Forests (BCF) Hahn, Murray, Carvalho (2020) <doi:10.1214/19-BA1195> for causal inference. Enables model serialization and parallel sampling and provides a low-level interface for custom stochastic forest samplers.

Maintained by Drew Herren. Last updated 6 hours ago.

bart bayesian-machine-learning bayesian-methods decision-trees gradient-boosted-trees machine-learning probabilistic-models tree-ensembles cpp

3.2 match 22 stars 8.57 score 40 scripts

r-lib

callr:Call R from R

It is sometimes useful to perform a computation in a separate R process, without affecting the current R process at all. This packages does exactly that.

Maintained by Gábor Csárdi. Last updated 23 days ago.

1.8 match 300 stars 15.28 score 289 scripts 1.2k dependents

baileych

srcr:Simplify Connections to Database Sources

Connecting to databases requires boilerplate code to specify connection parameters and to set up sessions properly with the DBMS. This package provides a simple tool to fill two purposes: abstracting connection details, including secret credentials, out of your source code and managing configuration for frequently-used database connections in a persistent and flexible way, while minimizing requirements on the runtime environment.

Maintained by Charles Bailey. Last updated 7 days ago.

6.6 match 1 stars 4.18 score 3 scripts

openanalytics

clinDataReview:Clinical Data Review Tool

Creation of interactive tables, listings and figures ('TLFs') and associated report for exploratory analysis of data in a clinical trial, e.g. for clinical oversight activities. Interactive figures include sunburst, treemap, scatterplot, line plot and barplot of counts data. Interactive tables include table of summary statistics (as counts of adverse events, enrollment table) and listings. Possibility to compare data (summary table or listing) across two data batches/sets. A clinical data review report is created via study-specific configuration files and template 'R Markdown' reports contained in the package.

Maintained by Laure Cougnaud. Last updated 9 months ago.

3.8 match 11 stars 7.10 score 36 scripts

fcampelo

MOEADr:Component-Wise MOEA/D Implementation

Modular implementation of Multiobjective Evolutionary Algorithms based on Decomposition (MOEA/D) [Zhang and Li (2007), <DOI:10.1109/TEVC.2007.892759>] for quick assembling and testing of new algorithmic components, as well as easy replication of published MOEA/D proposals. The full framework is documented in a paper published in the Journal of Statistical Software [<doi:10.18637/jss.v092.i06>].

Maintained by Felipe Campelo. Last updated 2 years ago.

moead multiobjective-optimization

4.3 match 20 stars 6.30 score 40 scripts

dyfanjones

RAthena:Connect to 'AWS Athena' using 'Boto3' ('DBI' Interface)

Designed to be compatible with the R package 'DBI' (Database Interface) when connecting to Amazon Web Service ('AWS') Athena <https://aws.amazon.com/athena/>. To do this 'Python' 'Boto3' Software Development Kit ('SDK') <https://boto3.amazonaws.com/v1/documentation/api/latest/index.html> is used as a driver.

Maintained by Dyfan Jones. Last updated 1 years ago.

athena aws boto3 database

3.8 match 37 stars 7.10 score 38 scripts

quarto-dev

quarto:R Interface to 'Quarto' Markdown Publishing System

Convert R Markdown documents and 'Jupyter' notebooks to a variety of output formats using 'Quarto'.

Maintained by Christophe Dervieux. Last updated 2 months ago.

1.8 match 147 stars 14.96 score 1.3k scripts 36 dependents

boettiger-lab

earthdatalogin:NASA 'EarthData' Access Utilities

Providing easy, portable access to NASA 'EarthData' products through the use of bearer tokens. Much of NASA's public data catalogs hosted and maintained by its 12 Distributed Active Archive Centers ('DAACs') are now made available on the Amazon Web Services 'S3' storage. However, accessing this data through the standard 'S3' API is restricted to only to compute resources running inside 'us-west-2' Data Center in Portland, Oregon, which allows NASA to avoid being charged data egress rates. This package provides public access to the data from any networked device by using the 'EarthData' login application programming interface (API), <https://www.earthdata.nasa.gov/eosdis/science-system-description/eosdis-components/earthdata-login>, providing convenient authentication and access to cloud-hosted NASA 'EarthData' products. This makes access to a wide range of earth observation data from any location straight forward and compatible with R packages that are widely used with cloud native earth observation data (such as 'terra', 'sf', etc.)

Maintained by Carl Boettiger. Last updated 29 days ago.

3.6 match 25 stars 7.37 score 42 scripts

allanvc

mRpostman:An IMAP Client for R

An easy-to-use IMAP client that provides tools for message searching, selective fetching of message attributes, mailbox management, attachment extraction, and several other IMAP features, paving the way for e-mail data analysis in R.

Maintained by Allan Quadros. Last updated 6 months ago.

4.5 match 31 stars 5.92 score 18 scripts

egenn

rtemis:Machine Learning and Visualization

Advanced Machine Learning and Visualization. Unsupervised Learning (Clustering, Decomposition), Supervised Learning (Classification, Regression), Cross-Decomposition, Bagging, Boosting, Meta-models. Static and interactive graphics.

Maintained by E.D. Gennatas. Last updated 1 months ago.

data-science data-visualization machine-learning machine-learning-library visualization

3.8 match 145 stars 7.09 score 50 scripts 2 dependents

pharmaverse

envsetup:Support the Setup of the R Environment for Clinical Trial Programming Workflows

The purpose of this package is to support the setup the R environment. The two main features are 'autos', to automatically source files and/or directories into your environment, and 'paths' to consistently set path objects across projects for input and output. Both are implemented using a configuration file to allow easy, custom configurations that can be used for multiple or all projects.

Maintained by Nicholas Masel. Last updated 9 months ago.

5.8 match 7 stars 4.54 score 5 scripts